RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17528
(366 letters)
>gnl|CDD|187547 cd05236, FAR-N_SDR_e, fatty acyl CoA reductases (FARs), extended
(e) SDRs. SDRs are Rossmann-fold NAD(P)H-binding
proteins, many of which may function as fatty acyl CoA
reductases (FAR), acting on medium and long chain fatty
acids, and have been reported to be involved in diverse
processes such as biosynthesis of insect pheromones,
plant cuticular wax production, and mammalian wax
biosynthesis. In Arabidopsis thaliana, proteins with
this particular architecture have also been identified
as the MALE STERILITY 2 (MS2) gene product, which is
implicated in male gametogenesis. Mutations in MS2
inhibit the synthesis of exine (sporopollenin),
rendering plants unable to reduce pollen wall fatty
acids to corresponding alcohols. This N-terminal domain
shares the catalytic triad (but not the upstream Asn)
and characteristic NADP-binding motif of the extended
SDR family. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 320
Score = 296 bits (761), Expect = 2e-99
Identities = 134/313 (42%), Positives = 170/313 (54%), Gaps = 31/313 (9%)
Query: 50 TIFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYNYFNDAVFDRMRLE 109
++ ITGATGFLG +L+EKLLR CP I KI LLIR + S +R+ D +FDR R
Sbjct: 2 SVLITGATGFLGKVLLEKLLRSCPDIGKIYLLIRGKSGQSAEERLRELLKDKLFDRGR-- 59
Query: 110 CPNYADKVDIGITHRVYNYFNDAVFDRMRLECPNYADKVDIVCGQLEADTFGLSARDEEL 169
N P + K+ + G L GLS D +
Sbjct: 60 -----------------NLN------------PLFESKIVPIEGDLSEPNLGLSDEDLQT 90
Query: 170 LISQTTIIFHIAATVRFDEHIRTAYNINVKGTQTILALAKRMKGLKSFVHVSTAYCNCDR 229
LI + II H AATV FDE + A +INV GT +L LAKR K LK+FVHVSTAY N DR
Sbjct: 91 LIEEVNIIIHCAATVTFDERLDEALSINVLGTLRLLELAKRCKKLKAFVHVSTAYVNGDR 150
Query: 230 KFIAEKFYPPVFTAEELSALVAHASDEEIALLNEHIIGGKPNSYTLTKATAEDLVRQVGH 289
+ I EK YPP E+L ++ D E+ ++GG PN+YT TKA AE LV +
Sbjct: 151 QLIEEKVYPPPADPEKLIDILELMDDLELERATPKLLGGHPNTYTFTKALAERLVLKERG 210
Query: 290 ELPICVLRPSIVFPTLQEPMPLWIKGFNGVMALALGAGTGLIRVVQTDPNISMDVVPGDR 349
LP+ ++RPSIV TL+EP P WI FNG L L G G++R + DPN D++P D
Sbjct: 211 NLPLVIVRPSIVGATLKEPFPGWIDNFNGPDGLFLAYGKGILRTMNADPNAVADIIPVDV 270
Query: 350 VINAMAALAWYFL 362
V NA+ A A Y
Sbjct: 271 VANALLAAAAYSG 283
>gnl|CDD|219687 pfam07993, NAD_binding_4, Male sterility protein. This family
represents the C-terminal region of the male sterility
protein in a number of arabidopsis and drosophila. A
sequence-related jojoba acyl CoA reductase is also
included.
Length = 245
Score = 218 bits (557), Expect = 1e-69
Identities = 98/304 (32%), Positives = 138/304 (45%), Gaps = 61/304 (20%)
Query: 53 ITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYNYFNDAVFDRMRLECPN 112
+TGATGFLG +L+EKLLR P++ KI L+R + S +R+
Sbjct: 1 LTGATGFLGKVLLEKLLRSTPEV-KIYCLVRAKDGESALERLRQ---------------- 43
Query: 113 YADKVDIGITHRVYNYFNDAVFDRMRLECPNYADKVDIVCGQLEADTFGLSARDEELLIS 172
+FDR++ +++ V G L GLS D + L
Sbjct: 44 --------------ELLKYGLFDRLK-----ALERIIPVAGDLSEPNLGLSDEDFQELAE 84
Query: 173 QTTIIFHIAATVRFDEHIRTAYNINVKGTQTILALAKRMKGLKSFVHVSTAYCNCDRKF- 231
+ +I H AATV F E NV GT+ +L LAK+MK F HVSTAY N +R
Sbjct: 85 EVDVIIHNAATVNFVEPYSDLRATNVLGTREVLRLAKQMK-KLPFHHVSTAYVNGERGGL 143
Query: 232 IAEKFYPPVFTAEELSALVAHASDEEIALLNEHIIGGKPNSYTLTKATAEDLVRQVGHEL 291
+ EK ++ ++GG PN YT +K AE LVR+ L
Sbjct: 144 LEEK-------------------PYKLDEDEPALLGGLPNGYTQSKWLAEQLVREAAGGL 184
Query: 292 PICVLRPSIVFPTLQEPMPLWIKGFN-GVMALALGAGTGLIRVVQTDPNISMDVVPGDRV 350
P+ + RPSI+ E WI G + G L GAG G++ + DP+ +D+VP D V
Sbjct: 185 PVVIYRPSIITG---ESRTGWINGDDFGPRGLLGGAGLGVLPDILGDPDARLDLVPVDYV 241
Query: 351 INAM 354
NA+
Sbjct: 242 ANAI 245
>gnl|CDD|215538 PLN02996, PLN02996, fatty acyl-CoA reductase.
Length = 491
Score = 165 bits (420), Expect = 8e-47
Identities = 102/343 (29%), Positives = 157/343 (45%), Gaps = 54/343 (15%)
Query: 39 LSPIQEFYKDQTIFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYNYF 98
+F +++TI +TGATGFL + VEK+LR P ++K+ LL+R + S TQR
Sbjct: 2 EGSCVQFLENKTILVTGATGFLAKIFVEKILRVQPNVKKLYLLLRASDAKSATQR----L 57
Query: 99 NDAVF--DRMRLECPNYADKVDIGITHRVYNYFNDAVFDRMRLECPNYADKVDIVCGQLE 156
+D V D ++ + ++ I+ +KV V G +
Sbjct: 58 HDEVIGKDLFKVLREKLGENLNSLIS-----------------------EKVTPVPGDIS 94
Query: 157 ADTFGLSARD-EELLISQTTIIFHIAATVRFDEHIRTAYNINVKGTQTILALAKRMKGLK 215
D G+ + E + + I+ ++AAT FDE A IN G +L AK+ +K
Sbjct: 95 YDDLGVKDSNLREEMWKEIDIVVNLAATTNFDERYDVALGINTLGALNVLNFAKKCVKVK 154
Query: 216 SFVHVSTAY-CNCDRKFIAEKFYP----------------PVFTAEELSALVAH-ASDEE 257
+HVSTAY C I EK + E+L L AS+EE
Sbjct: 155 MLLHVSTAYVCGEKSGLILEKPFHMGETLNGNRKLDINEEKKLVKEKLKELNEQDASEEE 214
Query: 258 IAL------LNEHIIGGKPNSYTLTKATAEDLVRQVGHELPICVLRPSIVFPTLQEPMPL 311
I + + G PN+Y TKA E L+ LP+ ++RP+++ T +EP P
Sbjct: 215 ITQAMKDLGMERAKLHGWPNTYVFTKAMGEMLLGNFKENLPLVIIRPTMITSTYKEPFPG 274
Query: 312 WIKGFNGVMALALGAGTGLIRVVQTDPNISMDVVPGDRVINAM 354
WI+G + ++ +G G G + DPN +DV+P D V+NAM
Sbjct: 275 WIEGLRTIDSVIVGYGKGKLTCFLADPNSVLDVIPADMVVNAM 317
>gnl|CDD|215279 PLN02503, PLN02503, fatty acyl-CoA reductase 2.
Length = 605
Score = 137 bits (347), Expect = 6e-36
Identities = 102/357 (28%), Positives = 157/357 (43%), Gaps = 69/357 (19%)
Query: 42 IQEFYKDQTIFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYNYFNDA 101
I EF + + ITGATGFL +L+EK+LR P + KI LLI+ + + +R+ N DA
Sbjct: 113 IAEFLRGKNFLITGATGFLAKVLIEKILRTNPDVGKIYLLIKAKDKEAAIERLKNEVIDA 172
Query: 102 -VFDRMRLECPNYADKVDIGITHRV-YNYFNDAVFDRMRLECPNYADKVDIVCGQLEADT 159
+F ++ TH Y F K+ V G +
Sbjct: 173 ELFKCLQE-------------THGKSYQSF--------------MLSKLVPVVGNVCESN 205
Query: 160 FGLSARDEELLISQTTIIFHIAATVRFDEHIRTAYNINVKGTQTILALAKRMKGLKSFVH 219
GL + + + +I + AA FDE A +IN +G +++ AK+ K LK F+
Sbjct: 206 LGLEPDLADEIAKEVDVIINSAANTTFDERYDVAIDINTRGPCHLMSFAKKCKKLKLFLQ 265
Query: 220 VSTAYCNCDRK------------FIAEKFYPPVFTAEELSALVAHASDEEIAL------- 260
VSTAY N R+ IA + AL A EI L
Sbjct: 266 VSTAYVNGQRQGRIMEKPFRMGDCIARELGISNSLPHNRPALDIEA---EIKLALDSKRH 322
Query: 261 ---------------LNEHIIGGKPNSYTLTKATAEDLVRQVGHELPICVLRPSIVFPTL 305
L + G ++Y TKA E ++ + ++P+ ++RPS++ T
Sbjct: 323 GFQSNSFAQKMKDLGLERAKLYGWQDTYVFTKAMGEMVINSMRGDIPVVIIRPSVIESTW 382
Query: 306 QEPMPLWIKGFNGVM-ALALGAGTGLIRVVQTDPNISMDVVPGDRVINA-MAALAWY 360
++P P W++G N +M + L G G + DPN +DVVP D V+NA +AA+A +
Sbjct: 383 KDPFPGWMEG-NRMMDPIVLYYGKGQLTGFLADPNGVLDVVPADMVVNATLAAMAKH 438
>gnl|CDD|187546 cd05235, SDR_e1, extended (e) SDRs, subgroup 1. This family
consists of an SDR module of multidomain proteins
identified as putative polyketide sythases fatty acid
synthases (FAS), and nonribosomal peptide synthases,
among others. However, unlike the usual ketoreductase
modules of FAS and polyketide synthase, these domains
are related to the extended SDRs, and have canonical
NAD(P)-binding motifs and an active site tetrad.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 290
Score = 99.3 bits (248), Expect = 6e-24
Identities = 70/258 (27%), Positives = 106/258 (41%), Gaps = 63/258 (24%)
Query: 50 TIFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYNYFNDAVFDRMRLE 109
T+ +TGATGFLG+ L+ +LL+ + KI L+R + + +R +
Sbjct: 1 TVLLTGATGFLGAYLLRELLKR-KNVSKIYCLVRAKDEEAALER------------LIDN 47
Query: 110 CPNYADKVDIGITHRVYNYFNDAVFDRMRLECPNYADKVDIVCGQLEADTFGLSARDEEL 169
Y + E ++ +V G L GLS D +
Sbjct: 48 LKEY--------------------GLNLWDE--LELSRIKVVVGDLSKPNLGLSDDDYQE 85
Query: 170 LISQTTIIFHIAATVRF---DEHIRTAYNINVKGTQTILALAKRMKGLKSFVHVSTAYCN 226
L + +I H A V + E ++ A NV GT+ +L LA K LK VST
Sbjct: 86 LAEEVDVIIHNGANVNWVYPYEELKPA---NVLGTKELLKLAATGK-LKPLHFVSTLS-- 139
Query: 227 CDRKFIAEKFYPPVFTAEELSALVAHASDEEIALLNEHIIGGKPNSYTLTKATAEDLVRQ 286
VF+AEE +AL SD+ + N G PN Y +K AE L+R+
Sbjct: 140 -------------VFSAEEYNALDDEESDDMLESQN-----GLPNGYIQSKWVAEKLLRE 181
Query: 287 VGHE-LPICVLRPSIVFP 303
+ LP+ ++RP +F
Sbjct: 182 AANRGLPVAIIRPGNIFG 199
>gnl|CDD|187573 cd05263, MupV_like_SDR_e, Pseudomonas fluorescens MupV-like,
extended (e) SDRs. This subgroup of extended SDR family
domains have the characteristic active site tetrad and a
well-conserved NAD(P)-binding motif. This subgroup is
not well characterized, its members are annotated as
having a variety of putative functions. One
characterized member is Pseudomonas fluorescens MupV a
protein involved in the biosynthesis of Mupirocin, a
polyketide-derived antibiotic. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 293
Score = 87.4 bits (217), Expect = 1e-19
Identities = 74/309 (23%), Positives = 116/309 (37%), Gaps = 77/309 (24%)
Query: 51 IFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYNYFNDAVFDRMRLEC 110
+F+TG TGFLG LV++LL K+++L+R+
Sbjct: 1 VFVTGGTGFLGRHLVKRLL---ENGFKVLVLVRSE------------------------- 32
Query: 111 PNYADKVDIGITHRVYNYFNDAVFDRMRLECPNYADKVDIVCGQLEADTFGLSARDEELL 170
+ E AD+V ++ G L GLSA L
Sbjct: 33 -------------------SLGEAHERIEEAGLEADRVRVLEGDLTQPNLGLSAAASREL 73
Query: 171 ISQTTIIFHIAATVRFDEHIRTAYNINVKGTQTILALAKRMKGLKSFVHVSTAYCNCDRK 230
+ + H AA+ F A+ N+ GT+ +L LA R ++ F +VSTAY +R
Sbjct: 74 AGKVDHVIHCAASYDFQAPNEDAWRTNIDGTEHVLELAAR-LDIQRFHYVSTAYVAGNR- 131
Query: 231 FIAEKFYPPVFTAEELSALVAHASDEEIALLNEHIIGGKPNSYTLTKATAEDLVRQVGHE 290
EL + N Y +KA AE LVR +
Sbjct: 132 -------EGNIRETEL--------NPGQNFKNP---------YEQSKAEAEQLVRAAATQ 167
Query: 291 LPICVLRPSIVFPTLQEPMPLWIKGFNGVMALALG-AGTGLIRVVQTDPNISMDVVPGDR 349
+P+ V RPSIV + + I+ +G+ L A G + + +++VP D
Sbjct: 168 IPLTVYRPSIV---VGDSKTGRIEKIDGLYELLNLLAKLGRWLPMPGNKGARLNLVPVDY 224
Query: 350 VINAMAALA 358
V +A+ L+
Sbjct: 225 VADAIVYLS 233
>gnl|CDD|225857 COG3320, COG3320, Putative dehydrogenase domain of multifunctional
non-ribosomal peptide synthetases and related enzymes
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 382
Score = 81.3 bits (201), Expect = 4e-17
Identities = 65/250 (26%), Positives = 92/250 (36%), Gaps = 58/250 (23%)
Query: 50 TIFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYNYFNDAVFDRMRLE 109
+ +TGATGFLG+ L+ +LL K+I L+R + ++A R+
Sbjct: 2 NVLLTGATGFLGAYLLLELLDRSD--AKVICLVRAQS------------DEAALARLEKT 47
Query: 110 CPNYADKVDIGITHRVYNYFNDAVFDRMRLECPNYADKVDIVCGQLEADTFGLSARDEEL 169
Y R ++ AD+V++V G L GLS R +
Sbjct: 48 FDLY----------RHWDEL--------------SADRVEVVAGDLAEPDLGLSERTWQE 83
Query: 170 LISQTTIIFHIAATVRFDEHIRTAYNINVKGTQTILALAKRMKGLKSFVHVSTAYCNCDR 229
L +I H AA V NV GT +L LA K K +VS+
Sbjct: 84 LAENVDLIIHNAALVNHVFPYSELRGANVLGTAEVLRLAATGKP-KPLHYVSS------- 135
Query: 230 KFIAEKFYPPVFTAEELSALVAHASDEEIALLNEHIIGGKPNSYTLTKATAEDLVRQ-VG 288
I+ V E S DE N + G Y +K AE LVR+
Sbjct: 136 --IS------VGETEYYSNFTV-DFDEISPTRN--VGQGLAGGYGRSKWVAEKLVREAGD 184
Query: 289 HELPICVLRP 298
LP+ + RP
Sbjct: 185 RGLPVTIFRP 194
>gnl|CDD|233557 TIGR01746, Thioester-redct, thioester reductase domain. This model
includes the terminal domain from the fungal alpha
aminoadipate reductase enzyme (also known as
aminoadipate semialdehyde dehydrogenase) which is
involved in the biosynthesis of lysine , as well as the
reductase-containing component of the myxochelin
biosynthetic gene cluster, MxcG. The mechanism of
reduction involves activation of the substrate by
adenylation and transfer to a covalently-linked
pantetheine cofactor as a thioester. This thioester is
then reduced to give an aldehyde (thus releasing the
product) and a regenerated pantetheine thiol. (In
myxochelin biosynthesis this aldehyde is further reduced
to an alcohol or converted to an amine by an
aminotransferase.) This is a fundamentally different
reaction than beta-ketoreductase domains of polyketide
synthases which act at a carbonyl two carbons removed
from the thioester and forms an alcohol as a product.
This domain is invariably found at the C-terminus of the
proteins which contain it (presumably because it results
in the release of the product). The majority of hits to
this model are non-ribosomal peptide synthetases in
which this domain is similarly located proximal to a
thiolation domain (pfam00550). In some cases this domain
is found at the end of a polyketide synthetase enzyme,
but is unlike ketoreductase domains which are found
before the thiolase domains. Exceptions to this observed
relationship with the thiolase domain include three
proteins which consist of stand-alone reductase domains
(GP|466833 from M. leprae, GP|435954 from Anabaena and
OMNI|NTL02SC1199 from Strep. coelicolor) and one protein
(OMNI|NTL01NS2636 from Nostoc) which contains N-terminal
homology with a small group of hypothetical proteins but
no evidence of a thiolation domain next to the putative
reductase domain. Below the noise cutoff to this model
are proteins containing more distantly related
ketoreductase and dehydratase/epimerase domains. It has
been suggested that a NADP-binding motif can be found in
the N-terminal portion of this domain that may form a
Rossman-type fold.
Length = 367
Score = 79.4 bits (196), Expect = 2e-16
Identities = 78/319 (24%), Positives = 121/319 (37%), Gaps = 83/319 (26%)
Query: 50 TIFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYNYFNDAV-FDRMRL 108
T+ +TGATGFLG+ L+E+LLR Q K+I L+R ++ +R+R
Sbjct: 1 TVLLTGATGFLGAYLLEELLRRSTQA-KVICLVRAA-------------SEEHAMERLRE 46
Query: 109 ECPNYADKVDIGITHRVYNYFNDAVFDRMRLECPNYA-DKVDIVCGQLEADTFGLSARDE 167
+Y RL + A +++++V G L GLS +
Sbjct: 47 ALRSY------------------------RLWHEDLARERIEVVAGDLSEPRLGLSDAEW 82
Query: 168 ELLISQTTIIFHIAATVRF---DEHIRTAYNINVKGTQTILALAKRMKGLKSFVHVSTAY 224
E L I H A V + +R A NV GT+ +L LA + K +VST
Sbjct: 83 ERLAENVDTIVHNGALVNWVYPYSELRGA---NVLGTREVLRLAASGRA-KPLHYVSTI- 137
Query: 225 CNCDRKFIAEKFYPPVFTAEELSALVAHASDEEIALLNEHIIGGKPNSYTLTKATAEDLV 284
V A +LS + E+ A + G Y +K AE LV
Sbjct: 138 --------------SVGAAIDLSTVT-----EDDATVTPPP--GLAGGYAQSKWVAELLV 176
Query: 285 RQVGHE-LPICVLRPSIVFPTLQ----EPMPLWIKGFNGVMALALGAGTGLIRVVQTDPN 339
R+ LP+ ++RP + + + G +AL P
Sbjct: 177 REASDRGLPVTIVRPGRILGNSYTGAINSSDILWRMVKGCLAL---------GAYPQSPE 227
Query: 340 ISMDVVPGDRVINAMAALA 358
++ D+ P D V A+ L+
Sbjct: 228 LTEDLTPVDFVARAIVVLS 246
>gnl|CDD|234212 TIGR03443, alpha_am_amid, L-aminoadipate-semialdehyde dehydrogenase.
Members of this protein family are
L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31),
product of the LYS2 gene. It is also called
alpha-aminoadipate reductase. In fungi, lysine is
synthesized via aminoadipate. Currently, all members of
this family are fungal.
Length = 1389
Score = 63.5 bits (155), Expect = 7e-11
Identities = 62/261 (23%), Positives = 101/261 (38%), Gaps = 57/261 (21%)
Query: 47 KDQTIFITGATGFLGSLLVEKLL-RCCPQIRKIILLIRTRGSTSITQRVYNYFNDAVFDR 105
T+F+TGATGFLGS ++ LL R K+ +R + +A +R
Sbjct: 970 TPITVFLTGATGFLGSFILRDLLTRRSNSNFKVFAHVRAKSE------------EAGLER 1017
Query: 106 MRLECPNYADKVDIGITHRVYNYFNDAVFDRMRLECPNYADKVDIVCGQLEADTFGLSAR 165
+R Y +++ +A ++++V G L + FGLS
Sbjct: 1018 LRKTG-------------TTYGIWDE-----------EWASRIEVVLGDLSKEKFGLSDE 1053
Query: 166 DEELLISQTTIIFHIAATVRFDEHIRTAYNINVKGTQTILALAKRMKGLKSFVHV-STAY 224
L ++ +I H A V + + NV GT +L L K K F V ST+
Sbjct: 1054 KWSDLTNEVDVIIHNGALVHWVYPYSKLRDANVIGTINVLNLCAEGKA-KQFSFVSSTSA 1112
Query: 225 CNCDRKFIAEKFYPPVFTAEELSALVAHASDEEIALLNEHIIG---GKPNSYTLTKATAE 281
+ + LS + A I ++ ++G G Y +K AE
Sbjct: 1113 LDTEYYV-------------NLSDELVQAGGAGI-PESDDLMGSSKGLGTGYGQSKWVAE 1158
Query: 282 DLVRQVGHE-LPICVLRPSIV 301
++R+ G L C++RP V
Sbjct: 1159 YIIREAGKRGLRGCIVRPGYV 1179
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 62.3 bits (151), Expect = 8e-11
Identities = 67/319 (21%), Positives = 96/319 (30%), Gaps = 106/319 (33%)
Query: 51 IFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYNYFNDAVFDRMRLEC 110
I +TG GF+GS LVE+LL G
Sbjct: 3 ILVTGGAGFIGSHLVERLLA--------------AG------------------------ 24
Query: 111 PNYADKVDIGITHRVYNYFNDAVFDRMRLECPNYADKVDIVCGQLEADTFGLSARDEELL 170
H V DR+R V+ V L +EL
Sbjct: 25 ------------HDVR------GLDRLRDGLDPLLSGVEFVVLDLTDRDL-----VDELA 61
Query: 171 ISQTTIIFHIAATVRF----DEHIRTAYNINVKGTQTILALAKRMKGLKSFVHVSTA--- 223
+ H+AA ++NV GT +L A+ G+K FV S+
Sbjct: 62 KGVPDAVIHLAAQSSVPDSNASDPAEFLDVNVDGTLNLLEAARAA-GVKRFVFASSVSVV 120
Query: 224 YCNCDRKFIAEKFYPPVFTAEELSALVAHASDEEIALLNEHIIGGKPNSYTLTKATAEDL 283
Y + I E PP N Y ++K AE L
Sbjct: 121 YGDPPPLPIDEDLGPPRPL----------------------------NPYGVSKLAAEQL 152
Query: 284 VRQVGHE--LPICVLRPSIVF-PTLQEPMPLWIKGFNGVMALALGAGTGL-IRVVQTDPN 339
+R LP+ +LRP V+ P + + + V A G I V+ D +
Sbjct: 153 LRAYARLYGLPVVILRPFNVYGPGDKPDLSSGV-----VSAFIRQLLKGEPIIVIGGDGS 207
Query: 340 ISMDVVPGDRVINAMAALA 358
+ D V D V +A+
Sbjct: 208 QTRDFVYVDDVADALLLAL 226
>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 57.7 bits (140), Expect = 4e-09
Identities = 77/334 (23%), Positives = 111/334 (33%), Gaps = 124/334 (37%)
Query: 50 TIFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYNYFNDAVFDRMRLE 109
F+TG TGF+G LV +LL + + +L+R R S S + + Y+
Sbjct: 2 RYFVTGGTGFIGRRLVSRLLDRRREAT-VHVLVR-RQSLSRLEALAAYWG---------- 49
Query: 110 CPNYADKVDIGITHRVYNYFNDAVFDRMRLECPNYADKVDIVCGQLEADTFGLSARDEEL 169
AD+V + G L GLS D
Sbjct: 50 -----------------------------------ADRVVPLVGDLTEPGLGLSEADIAE 74
Query: 170 LISQTTIIFHIAA----TVRFDEHIRTAYNINVKGTQTILALAKRMKGLKSFVHVSTAYC 225
L + H+AA T + NV GT+ ++ LA+R++ +F HVS+
Sbjct: 75 L-GDIDHVVHLAAIYDLTADEEAQRAA----NVDGTRNVVELAERLQA-ATFHHVSS--- 125
Query: 226 NCDRKFIA-EKFYPPVFTAEELSALVAHASDEEIALLNEHIIGGKPNSYTLTKATAEDLV 284
IA Y VF E+ + + P Y TK AE LV
Sbjct: 126 ------IAVAGDYEGVFR-------------EDDFDEGQGL----PTPYHRTKFEAEKLV 162
Query: 285 RQVGHELPICVLRPSIV------------------FPTLQ--EPMPLWIKGFNGVMALAL 324
R+ LP V RP++V F L +P W+ +
Sbjct: 163 REEC-GLPWRVYRPAVVVGDSRTGEMDKIDGPYYFFKVLAKLAKLPSWLP--------MV 213
Query: 325 GAGTGLIRVVQTDPNISMDVVPGDRVINAMAALA 358
G G NI VP D V +A+ L
Sbjct: 214 GPDGGRT-------NI----VPVDYVADALDHLM 236
>gnl|CDD|212494 cd08946, SDR_e, extended (e) SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 200
Score = 54.2 bits (131), Expect = 1e-08
Identities = 42/197 (21%), Positives = 72/197 (36%), Gaps = 54/197 (27%)
Query: 175 TIIFHIAATVRFDEHIRTA---YNINVKGTQTILALAKRMKGLKSFVHVSTA--YCNCDR 229
++ H+AA V + NV GT +L A++ G+K FV+ S+A Y + +
Sbjct: 32 DVVVHLAALVGVPASWDNPDEDFETNVVGTLNLLEAARKA-GVKRFVYASSASVYGSPEG 90
Query: 230 KFIAEKFYPPVFTAEELSALVAHASDEEIALLNEHIIGGKPNS-YTLTKATAEDLVRQVG 288
E+ P +P S Y ++K AE L+R G
Sbjct: 91 LPEEEETPP------------------------------RPLSPYGVSKLAAEHLLRSYG 120
Query: 289 --HELPICVLRPSIVF-----PTLQEPMPLWIKGFNGVMALALGAGTGLIRVVQTDPNIS 341
+ LP+ +LR + V+ P L + +I+ L + N +
Sbjct: 121 ESYGLPVVILRLANVYGPGQRPRLDGVVNDFIRRALEGKPLTVFG----------GGNQT 170
Query: 342 MDVVPGDRVINAMAALA 358
D + D V+ A+
Sbjct: 171 RDFIHVDDVVRAILHAL 187
Score = 39.6 bits (93), Expect = 0.001
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 51 IFITGATGFLGSLLVEKLLR 70
I +TG GF+GS LV +LL
Sbjct: 1 ILVTGGAGFIGSHLVRRLLE 20
>gnl|CDD|187539 cd05228, AR_FR_like_1_SDR_e, uncharacterized subgroup of aldehyde
reductase and flavonoid reductase related proteins,
extended (e) SDRs. This subgroup contains proteins of
unknown function related to aldehyde reductase and
flavonoid reductase of the extended SDR-type. Aldehyde
reductase I (aka carbonyl reductase) is an NADP-binding
SDR; it has an NADP-binding motif consensus that is
slightly different from the canonical SDR form and lacks
the Asn of the extended SDR active site tetrad. Aldehyde
reductase I catalyzes the NADP-dependent reduction of
ethyl 4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. The related flavonoid
reductases act in the NADP-dependent reduction of
flavonoids, ketone-containing plant secondary
metabolites. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 318
Score = 49.6 bits (119), Expect = 1e-06
Identities = 41/169 (24%), Positives = 58/169 (34%), Gaps = 41/169 (24%)
Query: 176 IIFHIAATVRF-DEHIRTAYNINVKGTQTILALAKRMKGLKSFVHVSTAYCNCDRKFIAE 234
+FH+AA + + Y NV+GT+ +L A G++ VH S+ IA
Sbjct: 65 RVFHLAAFTSLWAKDRKELYRTNVEGTRNVLDAALE-AGVRRVVHTSS---------IA- 113
Query: 235 KFYPPVFTAEELSALVAH---ASDEEIALLNEHIIGGKPNSYTLTKATAEDLVRQ-VGHE 290
AL DE PN Y +K AE V +
Sbjct: 114 -------------ALGGPPDGRIDET----TPWNERPFPNDYYRSKLLAELEVLEAAAEG 156
Query: 291 LPICVLRPSIVF------PTLQEPMPLWIKGFNGVMALALGAGTGLIRV 333
L + ++ PS VF PT L NG + GT + V
Sbjct: 157 LDVVIVNPSAVFGPGDEGPTSTGLDVLDY--LNGKLPAYPPGGTSFVDV 203
Score = 40.0 bits (94), Expect = 0.001
Identities = 14/20 (70%), Positives = 15/20 (75%)
Query: 51 IFITGATGFLGSLLVEKLLR 70
I +TGATGFLGS LV LL
Sbjct: 1 ILVTGATGFLGSNLVRALLA 20
>gnl|CDD|216461 pfam01370, Epimerase, NAD dependent epimerase/dehydratase family.
This family of proteins utilise NAD as a cofactor. The
proteins in this family use nucleotide-sugar substrates
for a variety of chemical reactions.
Length = 233
Score = 46.5 bits (111), Expect = 6e-06
Identities = 51/259 (19%), Positives = 74/259 (28%), Gaps = 97/259 (37%)
Query: 51 IFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYNYFNDAVFDRMRLEC 110
I +TG TGF+GS LV +LL+ I+L R R + T R+ R
Sbjct: 1 ILVTGGTGFIGSHLVRRLLQ--EGYEVIVLGRRRRSESLNTGRI------------RFHE 46
Query: 111 PNYADKVDIGITHRVYNYFNDAVFDRMRLECPNYADKVDIVCGQLEADTFGLSARDEELL 170
+ D + + + + D V
Sbjct: 47 GDLTDPDAL-----------ERLLAE---------VQPDAV------------------- 67
Query: 171 ISQTTIIFHIAATVRFDEHIRTA---YNINVKGTQTILALAKRMKGLKSFVHVSTA--YC 225
H+AA NV GT +L A+R G+K FV S++ Y
Sbjct: 68 -------IHLAAQSGVGASFEDPADFIRANVLGTLRLLEAARRA-GVKRFVFASSSEVYG 119
Query: 226 NCDRKFIAEKFYPPVFTAEELSALVAHASDEEIALLNEHIIGGKPNSYTLTKATAEDLVR 285
+ I E G + Y K AE LV
Sbjct: 120 DVADPPITEDTPL-----------------------------GPLSPYAAAKLAAERLVE 150
Query: 286 QVG--HELPICVLRPSIVF 302
+ L +LR V+
Sbjct: 151 AYARAYGLRAVILRLFNVY 169
>gnl|CDD|187548 cd05237, UDP_invert_4-6DH_SDR_e, UDP-Glcnac (UDP-linked
N-acetylglucosamine) inverting 4,6-dehydratase, extended
(e) SDRs. UDP-Glcnac inverting 4,6-dehydratase was
identified in Helicobacter pylori as the hexameric flaA1
gene product (FlaA1). FlaA1 is hexameric, possesses
UDP-GlcNAc-inverting 4,6-dehydratase activity, and
catalyzes the first step in the creation of a
pseudaminic acid derivative in protein glycosylation.
Although this subgroup has the NADP-binding motif
characteristic of extended SDRs, its members tend to
have a Met substituted for the active site Tyr found in
most SDR families. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 287
Score = 44.5 bits (106), Expect = 4e-05
Identities = 40/179 (22%), Positives = 62/179 (34%), Gaps = 54/179 (30%)
Query: 47 KDQTIFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYNYFNDAVFDRM 106
K +TI +TG G +GS LV ++L+ P +K+I+ R + + +
Sbjct: 1 KGKTILVTGGAGSIGSELVRQILKFGP--KKLIVF--DRDENKLHE-------------L 43
Query: 107 RLECPNYADKVDIGITHRVYNYFNDAVFDRMRLECPNYADKVDIVCGQLEADTFGLSARD 166
E + + + V D+ RL DIV
Sbjct: 44 VRELRSRFPHDKLR-------FIIGDVRDKERLRRAFKERGPDIV--------------- 81
Query: 167 EELLISQTTIIFHIAAT--VRFDEHIRT-AYNINVKGTQTILALAKRMKGLKSFVHVST 222
FH AA V E A NV GT+ ++ A G++ FV +ST
Sbjct: 82 -----------FHAAALKHVPSMEDNPEEAIKTNVLGTKNVIDAA-IENGVEKFVCIST 128
>gnl|CDD|187673 cd09813, 3b-HSD-NSDHL-like_SDR_e, human NSDHL (NAD(P)H steroid
dehydrogenase-like protein)-like, extended (e) SDRs.
This subgroup includes human NSDHL and related proteins.
These proteins have the characteristic active site
tetrad of extended SDRs, and also have a close match to
their NAD(P)-binding motif. Human NSDHL is a
3beta-hydroxysteroid dehydrogenase (3 beta-HSD) which
functions in the cholesterol biosynthetic pathway. 3
beta-HSD catalyzes the oxidative conversion of delta 5-3
beta-hydroxysteroids to the delta 4-3-keto
configuration; this activity is essential for the
biosynthesis of all classes of hormonal steroids.
Mutations in the gene encoding NSDHL cause CHILD
syndrome (congenital hemidysplasia with ichthyosiform
nevus and limb defects), an X-linked dominant,
male-lethal trait. This subgroup also includes an
unusual bifunctional [3beta-hydroxysteroid dehydrogenase
(3b-HSD)/C-4 decarboxylase from Arabidopsis thaliana,
and Saccharomyces cerevisiae ERG26, a 3b-HSD/C-4
decarboxylase, involved in the synthesis of ergosterol,
the major sterol of yeast. Extended SDRs are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid sythase have
a GGXGXXG NAD(P)-binding motif and an altered active
site motif (YXXXN). Fungal type ketoacyl reductases have
a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 335
Score = 43.5 bits (103), Expect = 1e-04
Identities = 64/286 (22%), Positives = 107/286 (37%), Gaps = 88/286 (30%)
Query: 50 TIFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYNYFNDAVFDRMRLE 109
+ + G +GFLG LVE+LLR RG+ ++ VFD
Sbjct: 1 SCLVVGGSGFLGRHLVEQLLR--------------RGNPTV----------HVFD----- 31
Query: 110 CPNYADKVDIGITHRVYNYFNDAVFDRMRLECPNYADKVDIVCGQLEADTFGLSARDEEL 169
I T + + + R++ + D D+ A +E
Sbjct: 32 ---------IRPTFEL----DPSSSGRVQFHTGDLTDPQDLE-----------KAFNE-- 65
Query: 170 LISQTTIIFHIAATVRFDEHIRTAYNINVKGTQTILALAKRMKGLKSFVHVSTAYCNCDR 229
++FH A+ + Y +NV+GT+ ++ A R G+K V+ S+A
Sbjct: 66 --KGPNVVFHTASPDH-GSNDDLYYKVNVQGTRNVIE-ACRKCGVKKLVYTSSASV---- 117
Query: 230 KFIAEKFYPPVFTAEELSALVAHASDEEIALLNEHIIGGKPNSYTLTKATAEDLVRQVGH 289
VF +++ DE + ++H ++Y TKA AE LV +
Sbjct: 118 ----------VFNGQDI-----INGDESLPYPDKHQ-----DAYNETKALAEKLVLKAND 157
Query: 290 ELP---ICVLRPSIVF-PTLQEPMPLWIKGF-NGVMALALGAGTGL 330
C LRP+ +F P ++ +P +K NG +G G L
Sbjct: 158 PESGLLTCALRPAGIFGPGDRQLVPGLLKAAKNGKTKFQIGDGNNL 203
>gnl|CDD|187557 cd05246, dTDP_GD_SDR_e, dTDP-D-glucose 4,6-dehydratase, extended
(e) SDRs. This subgroup contains dTDP-D-glucose
4,6-dehydratase and related proteins, members of the
extended-SDR family, with the characteristic Rossmann
fold core region, active site tetrad and NAD(P)-binding
motif. dTDP-D-glucose 4,6-dehydratase is closely related
to other sugar epimerases of the SDR family.
dTDP-D-dlucose 4,6,-dehydratase catalyzes the second of
four steps in the dTDP-L-rhamnose pathway (the
dehydration of dTDP-D-glucose to
dTDP-4-keto-6-deoxy-D-glucose) in the synthesis of
L-rhamnose, a cell wall component of some pathogenic
bacteria. In many gram negative bacteria, L-rhamnose is
an important constituent of lipopoylsaccharide
O-antigen. The larger N-terminal portion of
dTDP-D-Glucose 4,6-dehydratase forms a Rossmann fold
NAD-binding domain, while the C-terminus binds the sugar
substrate. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 315
Score = 42.9 bits (102), Expect = 2e-04
Identities = 46/169 (27%), Positives = 65/169 (38%), Gaps = 54/169 (31%)
Query: 165 RDEELLIS-----QTTIIFHIAATVRFD-------EHIRTAYNINVKGTQTILALAKRMK 212
D EL+ + + H AA D IRT NV GT T+L A++
Sbjct: 61 CDAELVDRLFEEEKIDAVIHFAAESHVDRSISDPEPFIRT----NVLGTYTLLEAARK-Y 115
Query: 213 GLKSFVHVSTAYCNCDRKFIAEKFYPPVFTAEEL--SALVAHASDEEIALLNEHIIGGKP 270
G+K FVH+ST +E+ L E L P
Sbjct: 116 GVKRFVHIST---------------------DEVYGDLLDDGEFTETSPL--------AP 146
Query: 271 NS-YTLTKATAEDLVR--QVGHELPICVLRPSIVFPTLQEP---MPLWI 313
S Y+ +KA A+ LVR + LP+ + R S + Q P +PL+I
Sbjct: 147 TSPYSASKAAADLLVRAYHRTYGLPVVITRCSNNYGPYQFPEKLIPLFI 195
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 43.0 bits (102), Expect = 2e-04
Identities = 46/191 (24%), Positives = 70/191 (36%), Gaps = 62/191 (32%)
Query: 39 LSPIQEFYKDQTIFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYNYF 98
I +T+ +TG G +GS L ++L+ P ++IIL +R + +
Sbjct: 241 TELIGAMLTGKTVLVTGGGGSIGSELCRQILKFNP--KEIILF--SRDEYKLYL-IDMEL 295
Query: 99 NDAVFDRMRLECPNYADKVDIGITHRVYNYFNDAVFDRMRLECPNYADKVDIVCGQLEAD 158
+ + P + IG V DR R+E KVDIV
Sbjct: 296 RE--------KFPELKLRFYIG-----------DVRDRDRVERAMEGHKVDIV------- 329
Query: 159 TFGLSARDEELLISQTTIIFHIAA-----TVRF--DEHIRTAYNINVKGTQTILALAKRM 211
FH AA V + +E I+T NV GT+ + A +
Sbjct: 330 -------------------FHAAALKHVPLVEYNPEEAIKT----NVLGTENVAEAAIK- 365
Query: 212 KGLKSFVHVST 222
G+K FV +ST
Sbjct: 366 NGVKKFVLIST 376
>gnl|CDD|216283 pfam01073, 3Beta_HSD, 3-beta hydroxysteroid dehydrogenase/isomerase
family. The enzyme 3 beta-hydroxysteroid
dehydrogenase/5-ene-4-ene isomerase (3 beta-HSD)
catalyzes the oxidation and isomerisation of 5-ene-3
beta-hydroxypregnene and 5-ene-hydroxyandrostene steroid
precursors into the corresponding 4-ene-ketosteroids
necessary for the formation of all classes of steroid
hormones.
Length = 280
Score = 41.6 bits (98), Expect = 4e-04
Identities = 33/136 (24%), Positives = 51/136 (37%), Gaps = 31/136 (22%)
Query: 176 IIFHIAATVRFDEHIR--TAYNINVKGTQTILALAKRMKGLKSFVHVSTAYCNCDRKFIA 233
++ H AA + T +NVKGTQ +L A G++ V+ S+ +
Sbjct: 69 VVIHTAAIIDVFGKAYRDTIMKVNVKGTQNVLD-ACVKAGVRVLVYTSSM----EVVG-- 121
Query: 234 EKFYPPVFTAEELSALVAHASDEEIALLNEHIIGGKPNSYTLTKATAEDLV-------RQ 286
P + + DE + H + Y +KA AE LV +
Sbjct: 122 -----PNSYGQPI-----VNGDETTPYESTH-----QDPYPESKALAEKLVLKANGSTLK 166
Query: 287 VGHELPICVLRPSIVF 302
G L C LRP+ +F
Sbjct: 167 NGGRLYTCALRPAGIF 182
Score = 28.1 bits (63), Expect = 6.7
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 53 ITGATGFLGSLLVEKLLRC--CPQIR 76
+TG GFLG +V LLR ++R
Sbjct: 2 VTGGGGFLGRHIVRLLLREGELQEVR 27
>gnl|CDD|187536 cd05193, AR_like_SDR_e, aldehyde reductase, flavonoid reductase,
and related proteins, extended (e) SDRs. This subgroup
contains aldehyde reductase and flavonoid reductase of
the extended SDR-type and related proteins. Proteins in
this subgroup have a complete SDR-type active site
tetrad and a close match to the canonical extended SDR
NADP-binding motif. Aldehyde reductase I (aka carbonyl
reductase) is an NADP-binding SDR; it catalyzes the
NADP-dependent reduction of ethyl
4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. The related flavonoid
reductases act in the NADP-dependent reduction of
flavonoids, ketone-containing plant secondary
metabolites. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 295
Score = 40.7 bits (95), Expect = 7e-04
Identities = 43/209 (20%), Positives = 62/209 (29%), Gaps = 37/209 (17%)
Query: 145 ADKVDIVCGQLE-------ADTFGLSARDE---ELLISQTTIIFHIAATVRF-----DEH 189
KV V L+ + DE + +I +FH+A V F +E
Sbjct: 32 PSKVKKVNHLLDLDAKPGRLELAVADLTDEQSFDEVIKGCAGVFHVATPVSFSSKDPNEV 91
Query: 190 IRTAYNINVKGTQTILALAKRMKGLKSFVHVSTAYCNCDRKFIAEKFYPPVFTAEELSAL 249
I+ + GT L A K +K FV S+A K E +E S
Sbjct: 92 IKP----AIGGTLNALKAAAAAKSVKRFVLTSSAGSVLIPKPNVEGIV-----LDEKS-- 140
Query: 250 VAHASDEEIALLNEHIIGGKPNSYTLTKATAEDLVRQVGHEL----PICVLRPSI---VF 302
+ EE + S TL + A + +L P +
Sbjct: 141 ---WNLEEFDSDPKKSAWVYAASKTLAEKAAWKFADENNIDLITVIPTLTIGTIFDSETP 197
Query: 303 PTLQEPMPLWIKGFNGVMALALGAGTGLI 331
+ M L I G GV G
Sbjct: 198 SSSGWAMSL-ITGNEGVSPALALIPPGYY 225
Score = 31.4 bits (71), Expect = 0.68
Identities = 10/17 (58%), Positives = 15/17 (88%)
Query: 53 ITGATGFLGSLLVEKLL 69
+TGA+GF+ S +VE+LL
Sbjct: 3 VTGASGFVASHVVEQLL 19
>gnl|CDD|187570 cd05260, GDP_MD_SDR_e, GDP-mannose 4,6 dehydratase, extended (e)
SDRs. GDP-mannose 4,6 dehydratase, a homodimeric SDR,
catalyzes the NADP(H)-dependent conversion of
GDP-(D)-mannose to GDP-4-keto, 6-deoxy-(D)-mannose in
the fucose biosynthesis pathway. These proteins have the
canonical active site triad and NAD-binding pattern,
however the active site Asn is often missing and may be
substituted with Asp. A Glu residue has been identified
as an important active site base. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 316
Score = 40.3 bits (95), Expect = 0.001
Identities = 44/199 (22%), Positives = 64/199 (32%), Gaps = 63/199 (31%)
Query: 50 TIFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYNYFNDAVFDRMRLE 109
ITG TG GS L E LL + ++ ++R S + + + Y N DR+ L
Sbjct: 1 RALITGITGQDGSYLAEFLLE---KGYEVHGIVRRSSSFNTDRIDHLYINK---DRITLH 54
Query: 110 CPNYADKVDIGITHRVYNYFNDAVFDRMRLECPNYADKVDIVCGQLEADTFGLSARDEEL 169
Y D D R
Sbjct: 55 ---YGDLTDSSSLRRAIE------------------------------------------ 69
Query: 170 LISQTTIIFHIAA----TVRFDEHIRTAYNINVKGTQTILALAKRMKGLKS-FVHVSTA- 223
+ I+H+AA V FD+ T +N GT +L A R+ GL + F S++
Sbjct: 70 -KVRPDEIYHLAAQSHVKVSFDDPEYT-AEVNAVGTLNLLE-AIRILGLDARFYQASSSE 126
Query: 224 -YCNCDRKFIAEK--FYPP 239
Y +E F P
Sbjct: 127 EYGKVQELPQSETTPFRPR 145
>gnl|CDD|200431 TIGR04180, EDH_00030, NAD dependent epimerase/dehydratase,
LLPSF_EDH_00030 family. This clade within the NAD
dependent epimerase/dehydratase superfamily (pfam01370)
is characterized by inclusion of its members within a
cassette of seven distinctive enzymes. These include
four genes homologous to the elements of the neuraminic
(sialic) acid biosynthesis cluster (NeuABCD), an
aminotransferase and a nucleotidyltransferase in
addition to the epimerase/dehydratase. Together it is
very likely that these enzymes direct the biosynthesis
of a nine-carbon sugar analagous to CMP-neuraminic acid.
These seven genes form the core of the cassette,
although they are often accompanied by additional genes
that may further modify the product sugar. Although this
cassette is widely distributed in bacteria, the family
nomenclature arises from the instance in Leptospira
interrogans serovar Lai, str. 56601, where it appears as
the 30th gene in the 91-gene lipopolysaccharide
biosynthesis cluster.
Length = 297
Score = 39.2 bits (92), Expect = 0.002
Identities = 42/176 (23%), Positives = 69/176 (39%), Gaps = 59/176 (33%)
Query: 51 IFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYNYFNDAVFDRMRLEC 110
+ +TGA GF+GS LVE L+R ++R +L YN FN
Sbjct: 1 VLVTGADGFIGSHLVEALVRQGYEVRAFVL--------------YNSFNSW--------- 37
Query: 111 PNYADKVDIGITHRVYNYFNDAVFDRMRLECPNYADKVDIVCGQL-EADTFGLSARDEEL 169
+ D P DK+++V G + + D+ + + +
Sbjct: 38 -GWLDTS-----------------------PPEVKDKIEVVTGDIRDPDSVRKAMKGCD- 72
Query: 170 LISQTTIIFHIAATVR--FDEHIRTAY-NINVKGTQTILALAKRMKGLKSFVHVST 222
++FH+AA + + +Y + NV GT +L A R G++ VH ST
Sbjct: 73 ------VVFHLAALIAIPYSYIAPDSYVDTNVTGTLNVLQ-AARDLGVEKVVHTST 121
>gnl|CDD|187562 cd05252, CDP_GD_SDR_e, CDP-D-glucose 4,6-dehydratase, extended (e)
SDRs. This subgroup contains CDP-D-glucose
4,6-dehydratase, an extended SDR, which catalyzes the
conversion of CDP-D-glucose to
CDP-4-keto-6-deoxy-D-glucose. This subgroup has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 336
Score = 39.2 bits (92), Expect = 0.002
Identities = 24/93 (25%), Positives = 42/93 (45%), Gaps = 13/93 (13%)
Query: 142 PNYADKVDIVCGQLEADTFGLSARDEELLI-----SQTTIIFHIAAT--VR--FDEHIRT 192
PN + ++ + T G RD L + I+FH+AA VR + + + T
Sbjct: 42 PNLFELANL--DNKISSTRG-DIRDLNALREAIREYEPEIVFHLAAQPLVRLSYKDPVET 98
Query: 193 AYNINVKGTQTILALAKRMKGLKSFVHVSTAYC 225
+ NV GT +L + +K+ V+V++ C
Sbjct: 99 -FETNVMGTVNLLEAIRETGSVKAVVNVTSDKC 130
Score = 37.3 bits (87), Expect = 0.009
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 45 FYKDQTIFITGATGFLGSLLVEKLL 69
F++ + + +TG TGF GS L L
Sbjct: 1 FWQGKRVLVTGHTGFKGSWLSLWLQ 25
>gnl|CDD|224013 COG1088, RfbB, dTDP-D-glucose 4,6-dehydratase [Cell envelope
biogenesis, outer membrane].
Length = 340
Score = 38.4 bits (90), Expect = 0.004
Identities = 30/113 (26%), Positives = 43/113 (38%), Gaps = 33/113 (29%)
Query: 190 IRTAYNINVKGTQTILALAKRMKGLKSFVHVSTAYCNCDRKFIAEKFYPPVFTAEELSAL 249
I+T NV GT T+L A++ G F H+ST D + FT E +
Sbjct: 98 IQT----NVVGTYTLLEAARKYWGKFRFHHIST-----DEVYGDLGLDDDAFT--ETTPY 146
Query: 250 VAHASDEEIALLNEHIIGGKPNS-YTLTKATAEDLVRQVGHE--LPICVLRPS 299
P+S Y+ +KA ++ LVR LP + R S
Sbjct: 147 -------------------NPSSPYSASKAASDLLVRAYVRTYGLPATITRCS 180
>gnl|CDD|187564 cd05254, dTDP_HR_like_SDR_e, dTDP-6-deoxy-L-lyxo-4-hexulose
reductase and related proteins, extended (e) SDRs.
dTDP-6-deoxy-L-lyxo-4-hexulose reductase, an extended
SDR, synthesizes dTDP-L-rhamnose from
alpha-D-glucose-1-phosphate, providing the precursor of
L-rhamnose, an essential cell wall component of many
pathogenic bacteria. This subgroup has the
characteristic active site tetrad and NADP-binding
motif. This subgroup also contains human MAT2B, the
regulatory subunit of methionine adenosyltransferase
(MAT); MAT catalyzes S-adenosylmethionine synthesis. The
human gene encoding MAT2B encodes two major splicing
variants which are induced in human cell liver cancer
and regulate HuR, an mRNA-binding protein which
stabilizes the mRNA of several cyclins, to affect cell
proliferation. Both MAT2B variants include this extended
SDR domain. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 280
Score = 38.0 bits (89), Expect = 0.004
Identities = 34/165 (20%), Positives = 54/165 (32%), Gaps = 40/165 (24%)
Query: 150 IVCGQLEADTFGLSARDEELLIS-----QTTIIFHIAATVRFDE---HIRTAYNINVKGT 201
I G+ A F L D + + + +I + AA R D+ AY +NV
Sbjct: 27 IGTGRSRASLFKLDLTDPDAVEEAIRDYKPDVIINCAAYTRVDKCESDPELAYRVNVLAP 86
Query: 202 QTILALAKRMKGLKSFVHVSTAYCNCDRKFIAEKFYPPVFTAEELSALVAHASDEEIALL 261
+ + AK + +H+ST Y VF ++ D L
Sbjct: 87 ENLARAAKEVGAR--LIHISTDY---------------VFDGKKGP---YKEEDAPNPL- 125
Query: 262 NEHIIGGKPNSYTLTKATAEDLVRQVGHELPICVLRPSIVFPTLQ 306
N Y +K E V +LR S ++ L+
Sbjct: 126 ---------NVYGKSKLLGEVAVLN--ANPRYLILRTSWLYGELK 159
>gnl|CDD|187537 cd05226, SDR_e_a, Extended (e) and atypical (a) SDRs. Extended
or atypical short-chain dehydrogenases/reductases
(SDRs, aka tyrosine-dependent oxidoreductases) are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
Atypical SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Atypical
SDRs include biliverdin IX beta reductase (BVR-B,aka
flavin reductase), NMRa (a negative transcriptional
regulator of various fungi), progesterone
5-beta-reductase like proteins, phenylcoumaran benzylic
ether and pinoresinol-lariciresinol reductases,
phenylpropene synthases, eugenol synthase,
triphenylmethane reductase, isoflavone reductases, and
others. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 176
Score = 36.2 bits (84), Expect = 0.009
Identities = 15/33 (45%), Positives = 20/33 (60%), Gaps = 3/33 (9%)
Query: 51 IFITGATGFLGSLLVEKLLRCCPQIRKIILLIR 83
I I GATGF+G L +LL Q ++ LL+R
Sbjct: 1 ILILGATGFIGRALARELLE---QGHEVTLLVR 30
>gnl|CDD|187552 cd05241, 3b-HSD-like_SDR_e, 3beta-hydroxysteroid dehydrogenases
(3b-HSD)-like, extended (e) SDRs. Extended SDR family
domains belonging to this subgroup have the
characteristic active site tetrad and a fairly
well-conserved NAD(P)-binding motif. 3b-HSD catalyzes
the NAD-dependent conversion of various steroids, such
as pregnenolone to progesterone, or androstenediol to
testosterone. This subgroup includes an unusual
bifunctional 3b-HSD/C-4 decarboxylase from Arabidopsis
thaliana, and Saccharomyces cerevisiae ERG26, a
3b-HSD/C-4 decarboxylase, involved in the synthesis of
ergosterol, the major sterol of yeast. It also includes
human 3 beta-HSD/HSD3B1 and C(27) 3beta-HSD/
[3beta-hydroxy-delta(5)-C(27)-steroid oxidoreductase;
HSD3B7]. C(27) 3beta-HSD/HSD3B7 is a membrane-bound
enzyme of the endoplasmic reticulum, that catalyzes the
isomerization and oxidation of 7alpha-hydroxylated
sterol intermediates, an early step in bile acid
biosynthesis. Mutations in the human NSDHL (NAD(P)H
steroid dehydrogenase-like protein) cause CHILD syndrome
(congenital hemidysplasia with ichthyosiform nevus and
limb defects), an X-linked dominant, male-lethal trait.
Mutations in the human gene encoding C(27) 3beta-HSD
underlie a rare autosomal recessive form of neonatal
cholestasis. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid sythase have
a GGXGXXG NAD(P)-binding motif and an altered active
site motif (YXXXN). Fungal type ketoacyl reductases have
a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 331
Score = 37.0 bits (86), Expect = 0.012
Identities = 56/291 (19%), Positives = 94/291 (32%), Gaps = 97/291 (33%)
Query: 50 TIFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYNYFNDAVFDRMRLE 109
++ +TG +GF G LV++LL RG T + R +
Sbjct: 1 SVLVTGGSGFFGERLVKQLLE--------------RGGTYV--RSF-------------- 30
Query: 110 CPNYADKVDIGITHRVYNYFNDAVFDRMRLECPNYADKVDIVCGQLEADTFGLSARDEEL 169
D G + + ++ + G + D E
Sbjct: 31 -----DIAPPGEALSAWQH-----------------PNIEFLKGDI------TDRNDVEQ 62
Query: 170 LISQTTIIFHIAATVRFDEHIRTAYNINVKGTQTILALAKRMKGLKSFVHVSTAYCNCDR 229
+S +FH AA V + +NV GTQ +L +R G++ FV+ S+
Sbjct: 63 ALSGADCVFHTAAIVPLAGPRDLYWEVNVGGTQNVLDACQRC-GVQKFVYTSS------- 114
Query: 230 KFIAEKFYP--PVFTAEELSALVAHASDEEIALLNEHIIGGKPNSYTLTKATAEDLVR-- 285
+ + + DE + + Y TKA AE +V
Sbjct: 115 ---SSVIFGGQNIHNG-----------DETLPYPPLDS-----DMYAETKAIAEIIVLEA 155
Query: 286 -QVGHELPICVLRPSIVF----PTLQEPMPLWIKGFNGVMALALGAGTGLI 331
+L C LRP+ +F L + W + G++ G G L+
Sbjct: 156 NGRD-DLLTCALRPAGIFGPGDQGLVPILFEWAE--KGLVKFVFGRGNNLV 203
>gnl|CDD|187572 cd05262, SDR_a7, atypical (a) SDRs, subgroup 7. This subgroup
contains atypical SDRs of unknown function. Members of
this subgroup have a glycine-rich NAD(P)-binding motif
consensus that matches the extended SDRs, TGXXGXXG, but
lacks the characteristic active site residues of the
SDRs. This subgroup has basic residues (HXXXR) in place
of the active site motif YXXXK, these may have a
catalytic role. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 291
Score = 36.6 bits (85), Expect = 0.015
Identities = 11/19 (57%), Positives = 17/19 (89%)
Query: 51 IFITGATGFLGSLLVEKLL 69
+F+TGATGF+GS +V +L+
Sbjct: 3 VFVTGATGFIGSAVVRELV 21
>gnl|CDD|215146 PLN02260, PLN02260, probable rhamnose biosynthetic enzyme.
Length = 668
Score = 36.3 bits (84), Expect = 0.027
Identities = 65/269 (24%), Positives = 93/269 (34%), Gaps = 82/269 (30%)
Query: 46 YKDQTIFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYNYFNDAVFDR 105
Y+ + I ITGA GF+ S + +L+R P KI++L
Sbjct: 4 YEPKNILITGAAGFIASHVANRLIRNYPDY-KIVVL------------------------ 38
Query: 106 MRLECPNYADKVDIGITHRVYNYFNDAVFDRMRLECPNYA-DKVDIVCGQLEADTFGLSA 164
DK+D + N PN+ K DI AD
Sbjct: 39 ---------DKLD--YCSNLKNLNPSK-------SSPNFKFVKGDIAS----ADLVNYLL 76
Query: 165 RDEELLISQTTIIFHIAATVRFDEHIRTAYNI---NVKGTQTILALAKRMKGLKSFVHVS 221
E + TI+ H AA D ++ N+ GT +L K ++ F+HVS
Sbjct: 77 ITEGI----DTIM-HFAAQTHVDNSFGNSFEFTKNNIYGTHVLLEACKVTGQIRRFIHVS 131
Query: 222 TAYCNCDRKFIAEKFYPPVFTAEELSALVAHASDEEIALLNEHIIGGKPNSYTLTKATAE 281
T V+ + A V + E LL N Y+ TKA AE
Sbjct: 132 T---------------DEVYGETDEDADVGNH--EASQLL-------PTNPYSATKAGAE 167
Query: 282 DLVRQVG--HELPICVLRPSIVFPTLQEP 308
LV G + LP+ R + V+ Q P
Sbjct: 168 MLVMAYGRSYGLPVITTRGNNVYGPNQFP 196
>gnl|CDD|176253 cd08293, PTGR2, Prostaglandin reductase. Prostaglandins and
related eicosanoids are metabolized by the oxidation of
the 15(S)-hydroxyl group of the NAD+-dependent (type I
15-PGDH) 15-prostaglandin dehydrogenase (15-PGDH)
followed by reduction by NADPH/NADH-dependent (type II
15-PGDH) delta-13 15-prostaglandin reductase (13-PGR) to
15-keto-13,14,-dihydroprostaglandins. 13-PGR is a
bifunctional enzyme, since it also has leukotriene B(4)
12-hydroxydehydrogenase activity. These 15-PGDH and
related enzymes are members of the medium chain
dehydrogenase/reductase family. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES.
Length = 345
Score = 35.8 bits (83), Expect = 0.027
Identities = 36/122 (29%), Positives = 50/122 (40%), Gaps = 36/122 (29%)
Query: 49 QTIFITGATGFLGSLL--VEKLLRC------CPQIRKIILLIRTRGSTSITQRVYNYFND 100
QT+ ++GA G GSL + +LL C C K LL G + NY D
Sbjct: 156 QTMVVSGAAGACGSLAGQIGRLLGCSRVVGICGSDEKCQLLKSELGFDA----AINYKTD 211
Query: 101 AVFDRMRLECPNYADKVDIGITHRVYNYFN-------DAVFDRMRLECPNYADKVDIVCG 153
V +R+R CP VD+ YF+ D V +M N + I+CG
Sbjct: 212 NVAERLRELCPE---GVDV--------YFDNVGGEISDTVISQM-----NENSHI-ILCG 254
Query: 154 QL 155
Q+
Sbjct: 255 QI 256
>gnl|CDD|187541 cd05230, UGD_SDR_e, UDP-glucuronate decarboxylase (UGD) and
related proteins, extended (e) SDRs. UGD catalyzes the
formation of UDP-xylose from UDP-glucuronate; it is an
extended-SDR, and has the characteristic glycine-rich
NAD-binding pattern, TGXXGXXG, and active site tetrad.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 305
Score = 35.7 bits (83), Expect = 0.029
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 49 QTIFITGATGFLGSLLVEKLLR 70
+ I ITG GFLGS L ++LL
Sbjct: 1 KRILITGGAGFLGSHLCDRLLE 22
>gnl|CDD|187538 cd05227, AR_SDR_e, aldehyde reductase, extended (e) SDRs. This
subgroup contains aldehyde reductase of the extended
SDR-type and related proteins. Aldehyde reductase I (aka
carbonyl reductase) is an NADP-binding SDR; it has an
NADP-binding motif consensus that is slightly different
from the canonical SDR form and lacks the Asn of the
extended SDR active site tetrad. Aldehyde reductase I
catalyzes the NADP-dependent reduction of ethyl
4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 301
Score = 35.3 bits (82), Expect = 0.039
Identities = 57/268 (21%), Positives = 94/268 (35%), Gaps = 83/268 (30%)
Query: 50 TIFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYNYFNDAVFDRMRLE 109
+ +TGATGF+ S +VE+LL+ K+ +R S S + ++ A+
Sbjct: 1 LVLVTGATGFIASHIVEQLLK---AGYKVRGTVR---SLSKSAKL-----KALLK----- 44
Query: 110 CPNYADKVDIGITHRVYNYFNDAVFDRMRLECPNYADKVDIVCGQLEADTFGLSARDEEL 169
Y D+++ I V + +D VD V
Sbjct: 45 AAGYNDRLEFVI---VDDLTAPNAWD-------EALKGVDYVI----------------- 77
Query: 170 LISQTTIIFHIAATVRF------DEHIRTAYNINVKGTQTILALAKRMKGLKSFVHVSTA 223
H+A+ F D+ I A V+GT +L AK +K V S+
Sbjct: 78 ---------HVASPFPFTGPDAEDDVIDPA----VEGTLNVLEAAKAAGSVKRVVLTSSV 124
Query: 224 YCNCDRKFIAEKFYPPVFTAEELSALVAHASDEEIALLNEHIIGGKPNSYTLTKATAE-- 281
D AE VFT E+ + L S+ ++Y +K AE
Sbjct: 125 AAVGD--PTAED-PGKVFTEEDWNDLTISKSN-------------GLDAYIASKTLAEKA 168
Query: 282 --DLVRQVGHELPICVLRPSIVF-PTLQ 306
+ V++ + + + P V P+L
Sbjct: 169 AWEFVKENKPKFELITINPGYVLGPSLL 196
>gnl|CDD|163279 TIGR03466, HpnA, hopanoid-associated sugar epimerase. The
sequences in this family are members of the pfam01370
superfamily of NAD-dependent epimerases and dehydratases
typically acting on nucleotide-sugar substrates. The
genes of the family modeled here are generally in the
same locus with genes involved in the biosynthesis and
elaboration of hopene, the cyclization product of the
polyisoprenoid squalene. This gene and its association
with hopene biosynthesis in Zymomonas mobilis has been
noted in the literature where the gene symbol hpnA was
assigned. Hopanoids are known to be components of the
plasma membrane and to have polar sugar head groups in
Z. mobilis and other species.
Length = 328
Score = 35.4 bits (82), Expect = 0.040
Identities = 30/134 (22%), Positives = 48/134 (35%), Gaps = 41/134 (30%)
Query: 176 IIFHIAATVRF---DEHIRTAYNINVKGTQTILALAKRMKGLKSFVHVSTAYCNCDRKFI 232
+FH+AA R D Y NV+GT+ +L A G++ V+ S+
Sbjct: 67 ALFHVAADYRLWAPDP--EEMYAANVEGTRNLL-RAALEAGVERVVYTSSV--------- 114
Query: 233 AEKFYPPVFTAEELSALVAHASDEEIA-----LLNEHIIGGKPNSYTLTKATAEDLVRQV 287
A + D A + +IG Y +K AE ++
Sbjct: 115 ---------------ATLGVRGDGTPADETTPSSLDDMIG----HYKRSKFLAEQAALEM 155
Query: 288 GHE--LPICVLRPS 299
E LP+ ++ PS
Sbjct: 156 AAEKGLPVVIVNPS 169
Score = 31.9 bits (73), Expect = 0.52
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 50 TIFITGATGFLGSLLVEKLL 69
+ +TGATGF+GS +V LL
Sbjct: 2 KVLVTGATGFVGSAVVRLLL 21
>gnl|CDD|132628 TIGR03589, PseB, UDP-N-acetylglucosamine 4,6-dehydratase. This
enzyme catalyzes the first step in the biosynthesis of
pseudaminic acid, the conversion of
UDP-N-acetylglucosamine to
UDP-4-keto-6-deoxy-N-acetylglucosamine. These sequences
are members of the broader pfam01073 (3-beta
hydroxysteroid dehydrogenase/isomerase family) family.
Length = 324
Score = 35.5 bits (82), Expect = 0.040
Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 6/70 (8%)
Query: 45 FYKDQTIFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYN-----YFN 99
+ +++I ITG TG G + +LL +KII+ R Q+ + +F
Sbjct: 1 MFNNKSILITGGTGSFGKAFISRLLENY-NPKKIIIYSRDELKQWEMQQKFPAPCLRFFI 59
Query: 100 DAVFDRMRLE 109
V D+ RL
Sbjct: 60 GDVRDKERLT 69
>gnl|CDD|187567 cd05257, Arna_like_SDR_e, Arna decarboxylase_like, extended (e)
SDRs. Decarboxylase domain of ArnA. ArnA, is an enzyme
involved in the modification of outer membrane protein
lipid A of gram-negative bacteria. It is a bifunctional
enzyme that catalyzes the NAD-dependent decarboxylation
of UDP-glucuronic acid and
N-10-formyltetrahydrofolate-dependent formylation of
UDP-4-amino-4-deoxy-l-arabinose; its NAD-dependent
decaboxylating activity is in the C-terminal 360
residues. This subgroup belongs to the extended SDR
family, however the NAD binding motif is not a perfect
match and the upstream Asn of the canonical active site
tetrad is not conserved. Extended SDRs are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 316
Score = 34.6 bits (80), Expect = 0.059
Identities = 12/21 (57%), Positives = 16/21 (76%)
Query: 50 TIFITGATGFLGSLLVEKLLR 70
+ +TGA GF+GS L E+LLR
Sbjct: 1 NVLVTGADGFIGSHLTERLLR 21
Score = 29.6 bits (67), Expect = 2.7
Identities = 19/71 (26%), Positives = 27/71 (38%), Gaps = 6/71 (8%)
Query: 170 LISQTTIIFHIAATVRFDEHIRTAY---NINVKGTQTILALAKRMKGLKSFVHVSTA--Y 224
L+ + ++FH+AA + NV GT +L A K VH ST+ Y
Sbjct: 65 LVKKCDVVFHLAALIAIPYSYTAPLSYVETNVFGTLNVLEAACV-LYRKRVVHTSTSEVY 123
Query: 225 CNCDRKFIAEK 235
I E
Sbjct: 124 GTAQDVPIDED 134
>gnl|CDD|187551 cd05240, UDP_G4E_3_SDR_e, UDP-glucose 4 epimerase (G4E), subgroup
3, extended (e) SDRs. Members of this bacterial
subgroup are identified as possible sugar epimerases,
such as UDP-glucose 4 epimerase. However, while the
NAD(P)-binding motif is fairly well conserved, not all
members retain the canonical active site tetrad of the
extended SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 306
Score = 34.7 bits (80), Expect = 0.067
Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 51 IFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVY 95
I +TGA G LG LL +L P++ + L R R S + Y
Sbjct: 1 ILVTGAAGGLGRLLARRLAA-SPRVIGVDGLDRRRPPGSPPKVEY 44
Score = 28.5 bits (64), Expect = 5.1
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 1/45 (2%)
Query: 179 HIAATVRFDEHIRTAYNINVKGTQTILALAKRMKGLKSFVHVSTA 223
H+A + + INV GTQ +L G+ V S+
Sbjct: 68 HLAFILDPPRDGAERHRINVDGTQNVLDACAA-AGVPRVVVTSSV 111
>gnl|CDD|217199 pfam02719, Polysacc_synt_2, Polysaccharide biosynthesis protein.
This is a family of diverse bacterial polysaccharide
biosynthesis proteins including the CapD protein, WalL
protein mannosyl-transferase and several putative
epimerases (e.g. WbiI).
Length = 280
Score = 34.0 bits (79), Expect = 0.087
Identities = 43/181 (23%), Positives = 65/181 (35%), Gaps = 66/181 (36%)
Query: 51 IFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYNYFNDAVFDRMRLEC 110
+ +TG G +GS L ++L+ +KIIL +R + + +R E
Sbjct: 1 VLVTGGGGSIGSELCRQILKF--NPKKIILF--SRDEFKL---------YEIRQELRQEY 47
Query: 111 PNYADKVDIGITHRVYNYFNDAVFDRMRLE--CPNYADKVDIVCGQLEADTFGLSARDEE 168
+ + IG V DR RLE + VD V
Sbjct: 48 NDPKLRFFIG-----------DVRDRERLERAMEQH--GVDTV----------------- 77
Query: 169 LLISQTTIIFHIAA-----TVRFD--EHIRTAYNINVKGTQTILALAKRMKGLKSFVHVS 221
FH AA V ++ E I+T NV GT+ + A G++ FV +S
Sbjct: 78 ---------FHAAALKHVPLVEYNPMEAIKT----NVLGTENVAEAAIEN-GVEKFVLIS 123
Query: 222 T 222
T
Sbjct: 124 T 124
>gnl|CDD|187553 cd05242, SDR_a8, atypical (a) SDRs, subgroup 8. This subgroup
contains atypical SDRs of unknown function. Proteins in
this subgroup have a glycine-rich NAD(P)-binding motif
consensus that resembles that of the extended SDRs,
(GXXGXXG or GGXGXXG), but lacks the characteristic
active site residues of the SDRs. A Cys often replaces
the usual Lys of the YXXXK active site motif, while the
upstream Ser is generally present and Arg replaces the
usual Asn. Atypical SDRs generally lack the catalytic
residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 296
Score = 33.4 bits (77), Expect = 0.15
Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 3/47 (6%)
Query: 50 TIFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYN 96
I ITG TGF+G L +L ++++L R G V
Sbjct: 1 KIVITGGTGFIGRALTRRLTA---AGHEVVVLSRRPGKAEGLAEVIT 44
>gnl|CDD|187554 cd05243, SDR_a5, atypical (a) SDRs, subgroup 5. This subgroup
contains atypical SDRs, some of which are identified as
putative NAD(P)-dependent epimerases, one as a putative
NAD-dependent epimerase/dehydratase. Atypical SDRs are
distinct from classical SDRs. Members of this subgroup
have a glycine-rich NAD(P)-binding motif that is very
similar to the extended SDRs, GXXGXXG, and binds NADP.
Generally, this subgroup has poor conservation of the
active site tetrad; however, individual sequences do
contain matches to the YXXXK active site motif, the
upstream Ser, and there is a highly conserved Asp in
place of the usual active site Asn throughout the
subgroup. Atypical SDRs generally lack the catalytic
residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 203
Score = 33.0 bits (76), Expect = 0.17
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 50 TIFITGATGFLGSLLVEKLLR 70
+ + GATG +G +V +LL
Sbjct: 1 KVLVVGATGKVGRHVVRELLD 21
>gnl|CDD|187545 cd05234, UDP_G4E_2_SDR_e, UDP-glucose 4 epimerase, subgroup 2,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup is comprised of
archaeal and bacterial proteins, and has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 305
Score = 33.0 bits (76), Expect = 0.18
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 51 IFITGATGFLGSLLVEKLLR 70
I +TG GF+GS LV++LL
Sbjct: 2 ILVTGGAGFIGSHLVDRLLE 21
>gnl|CDD|187661 cd08958, FR_SDR_e, flavonoid reductase (FR), extended (e) SDRs.
This subgroup contains FRs of the extended SDR-type and
related proteins. These FRs act in the NADP-dependent
reduction of flavonoids, ketone-containing plant
secondary metabolites; they have the characteristic
active site triad of the SDRs (though not the upstream
active site Asn) and a NADP-binding motif that is very
similar to the typical extended SDR motif. Extended
SDRs are distinct from classical SDRs. In addition to
the Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 293
Score = 32.9 bits (76), Expect = 0.18
Identities = 11/17 (64%), Positives = 16/17 (94%)
Query: 54 TGATGFLGSLLVEKLLR 70
TGA+GF+GS LV++LL+
Sbjct: 4 TGASGFIGSWLVKRLLQ 20
>gnl|CDD|215072 PLN00141, PLN00141, Tic62-NAD(P)-related group II protein;
Provisional.
Length = 251
Score = 32.9 bits (75), Expect = 0.19
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 35 SDETLSPIQEFYKDQTIFITGATGFLGSLLVEKLL 69
E E K +T+F+ GATG G +VE+LL
Sbjct: 4 GAEASEEDAENVKTKTVFVAGATGRTGKRIVEQLL 38
>gnl|CDD|236399 PRK09186, PRK09186, flagellin modification protein A;
Provisional.
Length = 256
Score = 32.7 bits (75), Expect = 0.23
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 47 KDQTIFITGATGFLGSLLVEKLL 69
K +TI ITGA G +GS LV+ +L
Sbjct: 3 KGKTILITGAGGLIGSALVKAIL 25
>gnl|CDD|130249 TIGR01181, dTDP_gluc_dehyt, dTDP-glucose 4,6-dehydratase. This
protein is related to UDP-glucose 4-epimerase (GalE) and
likewise has an NAD cofactor [Cell envelope,
Biosynthesis and degradation of surface polysaccharides
and lipopolysaccharides].
Length = 317
Score = 32.7 bits (75), Expect = 0.25
Identities = 55/261 (21%), Positives = 78/261 (29%), Gaps = 94/261 (36%)
Query: 50 TIFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYNYFNDAVFDRMRL- 108
I +TG GF+GS V +L P I+L T + L
Sbjct: 1 RILVTGGAGFIGSNFVRYILNEHPDAEVIVLDKLTYAG----------------NLENLA 44
Query: 109 ---ECPNYA-DKVDIGITHRVYNYFNDAVFDRMRLECPNYADKVDIVCGQLEADTFGLSA 164
+ P Y K DIG DR + V + + + D
Sbjct: 45 DLEDNPRYRFVKGDIG--------------DR---------ELVSRLFTEHQPDA----- 76
Query: 165 RDEELLISQTTIIFHIAATVRFDEHIRTAY---NINVKGTQTILALAKRMKGLKSFVHVS 221
+ H AA D I NV GT T+L ++ F H+S
Sbjct: 77 ------------VVHFAAESHVDRSISGPAAFIETNVVGTYTLLEAVRKYWHEFRFHHIS 124
Query: 222 TAYCNCDRKFIAEKFYPPVFTAEELSALVAHASDEEIALLNEHIIGGKPNS-YTLTKATA 280
T ++ Y A E L P+S Y+ +KA +
Sbjct: 125 T-----------DEVYG--------DLEKGDAFTETTPL--------APSSPYSASKAAS 157
Query: 281 EDLVRQVGHE--LPICVLRPS 299
+ LVR LP + R S
Sbjct: 158 DHLVRAYHRTYGLPALITRCS 178
>gnl|CDD|233954 TIGR02622, CDP_4_6_dhtase, CDP-glucose 4,6-dehydratase. Members
of this protein family are CDP-glucose 4,6-dehydratase
from a variety of Gram-negative and Gram-positive
bacteria. Members typically are encoded next to a gene
that encodes a glucose-1-phosphate
cytidylyltransferase, which produces the substrate,
CDP-D-glucose, used by this enzyme to produce
CDP-4-keto-6-deoxyglucose [Cell envelope, Biosynthesis
and degradation of surface polysaccharides and
lipopolysaccharides].
Length = 349
Score = 32.7 bits (75), Expect = 0.26
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 45 FYKDQTIFITGATGFLGSLLV 65
F++ + + +TG TGF GS L
Sbjct: 1 FWQGKKVLVTGHTGFKGSWLS 21
Score = 31.9 bits (73), Expect = 0.48
Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 10/70 (14%)
Query: 165 RDEELLI-----SQTTIIFHIAAT--VR--FDEHIRTAYNINVKGTQTILALAKRMKGLK 215
RD L + I+FH+AA VR + + + T + NV GT +L + + +K
Sbjct: 62 RDAAKLRKAIAEFKPEIVFHLAAQPLVRKSYADPLET-FETNVMGTVNLLEAIRAIGSVK 120
Query: 216 SFVHVSTAYC 225
+ V+V++ C
Sbjct: 121 AVVNVTSDKC 130
>gnl|CDD|178256 PLN02650, PLN02650, dihydroflavonol-4-reductase.
Length = 351
Score = 32.9 bits (75), Expect = 0.27
Identities = 12/21 (57%), Positives = 18/21 (85%)
Query: 49 QTIFITGATGFLGSLLVEKLL 69
+T+ +TGA+GF+GS LV +LL
Sbjct: 6 ETVCVTGASGFIGSWLVMRLL 26
>gnl|CDD|223774 COG0702, COG0702, Predicted nucleoside-diphosphate-sugar
epimerases [Cell envelope biogenesis, outer membrane /
Carbohydrate transport and metabolism].
Length = 275
Score = 32.2 bits (73), Expect = 0.31
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 51 IFITGATGFLGSLLVEKLLR 70
I +TGATGF+G +V +LL
Sbjct: 3 ILVTGATGFVGGAVVRELLA 22
>gnl|CDD|187543 cd05232, UDP_G4E_4_SDR_e, UDP-glucose 4 epimerase, subgroup 4,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup is comprised of
bacterial proteins, and includes the Staphylococcus
aureus capsular polysaccharide Cap5N, which may have a
role in the synthesis of UDP-N-acetyl-d-fucosamine. This
subgroup has the characteristic active site tetrad and
NAD-binding motif of the extended SDRs. Extended SDRs
are distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 303
Score = 31.9 bits (73), Expect = 0.44
Identities = 27/141 (19%), Positives = 52/141 (36%), Gaps = 36/141 (25%)
Query: 170 LISQTTIIFHIAATVRFDEHIRTAYN------INVKGTQTILALAKRMKGLKSFVHVSTA 223
L + H+AA V + + A +N + T+ + A R +G+K FV +S+
Sbjct: 54 LFLGVDAVVHLAARV-HVMNDQGADPLSDYRKVNTELTRRLARAAAR-QGVKRFVFLSSV 111
Query: 224 YCNCDRKFIAEKFYPPVFTAEELSALVAHASDEEIALLNEHIIGGKPNSYTLTKATAEDL 283
K E + A + + + Y +K AE
Sbjct: 112 ------KVNGE------------GTVGAPFDETDPPAPQDA--------YGRSKLEAERA 145
Query: 284 VRQVGHE--LPICVLRPSIVF 302
+ ++G + + +LRP +V+
Sbjct: 146 LLELGASDGMEVVILRPPMVY 166
Score = 31.9 bits (73), Expect = 0.51
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 50 TIFITGATGFLGSLLVEKLL 69
+ +TGA GF+G LV+KLL
Sbjct: 1 KVLVTGANGFIGRALVDKLL 20
>gnl|CDD|131703 TIGR02655, circ_KaiC, circadian clock protein KaiC. Members of
this family are the circadian clock protein KaiC, part
of the kaiABC operon that controls circadian rhythm. It
may be universal in Cyanobacteria. Each member has two
copies of the KaiC domain (pfam06745), which is also
found in other proteins. KaiC performs
autophosphorylation and acts as its own transcriptional
repressor [Cellular processes, Other].
Length = 484
Score = 32.2 bits (73), Expect = 0.48
Identities = 21/63 (33%), Positives = 29/63 (46%), Gaps = 3/63 (4%)
Query: 45 FYKDQTIFITGATGFLGSLLVEKLLR-CCPQIRKIILLIRTRGSTSITQRVYNYFNDAVF 103
F+KD I TGATG +LLV K L C + IL + + Y++ D F
Sbjct: 260 FFKDSIILATGATGTGKTLLVSKFLENACANKERAILFAYEESRAQLLRNAYSWGID--F 317
Query: 104 DRM 106
+ M
Sbjct: 318 EEM 320
>gnl|CDD|224016 COG1091, RfbD, dTDP-4-dehydrorhamnose reductase [Cell envelope
biogenesis, outer membrane].
Length = 281
Score = 31.9 bits (73), Expect = 0.50
Identities = 30/132 (22%), Positives = 45/132 (34%), Gaps = 38/132 (28%)
Query: 176 IIFHIAATVRFD---EHIRTAYNINVKGTQTILALAKRMKGLKSFVHVSTAYCNCDRKFI 232
++ + AA D A+ +N G + + A + G + VH+ST Y
Sbjct: 53 VVINAAAYTAVDKAESEPELAFAVNATGAENLARAAAEV-GAR-LVHISTDY-------- 102
Query: 233 AEKFYPPVFTAEELSALVAHASDEEIALLNEHIIGGKPNSYTLTKATAEDLVRQVG--HE 290
VF E+ D L N Y +K E+ VR G H
Sbjct: 103 -------VFDGEKGGPYKET--DTPNPL----------NVYGRSKLAGEEAVRAAGPRHL 143
Query: 291 LPICVLRPSIVF 302
+LR S V+
Sbjct: 144 ----ILRTSWVY 151
>gnl|CDD|187579 cd05271, NDUFA9_like_SDR_a, NADH dehydrogenase (ubiquinone) 1 alpha
subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical
(a) SDRs. This subgroup of extended SDR-like proteins
are atypical SDRs. They have a glycine-rich
NAD(P)-binding motif similar to the typical SDRs,
GXXGXXG, and have the YXXXK active site motif (though
not the other residues of the SDR tetrad). Members
identified include NDUFA9 (mitochondrial) and putative
nucleoside-diphosphate-sugar epimerase. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 273
Score = 31.8 bits (73), Expect = 0.50
Identities = 47/256 (18%), Positives = 79/256 (30%), Gaps = 107/256 (41%)
Query: 50 TIFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSI--TQRVYNYFNDAVFDRMR 107
+ + GATGF+G +V +L + RGS I + R
Sbjct: 2 VVTVFGATGFIGRYVVNRLAK--------------RGSQVIVPYRCEAYA--------RR 39
Query: 108 LECPNYADKVDIGITHRVYNYFNDAVFDRMRLECPNYADKVDIVCGQLEADTFGLSARDE 167
L +V ++ +D + + D+V L R
Sbjct: 40 LLVMGDLGQVLF----VEFDLRDDESIRKA-------LEGSDVV--------INLVGRLY 80
Query: 168 ELLISQTTIIFHIAATVRFDEHIRTAYNINVKGTQTILALAKRMKGLKSFVHVSTAYCNC 227
E T F + +++V+G + + AK G++ +H+
Sbjct: 81 E--------------TKNF-----SFEDVHVEGPERLAKAAKEA-GVERLIHI------- 113
Query: 228 DRKFIAEKFYPPVFTAEELSALVAHASDEEIALLNEHIIGGKPNSYTLTKATAEDLVRQV 287
SAL A A+ P+ Y +KA E+ VR+
Sbjct: 114 -------------------SALGADANS--------------PSKYLRSKAEGEEAVRE- 139
Query: 288 GHELPICV-LRPSIVF 302
P +RPS+VF
Sbjct: 140 --AFPEATIVRPSVVF 153
>gnl|CDD|187581 cd05273, GME-like_SDR_e, Arabidopsis thaliana
GDP-mannose-3',5'-epimerase (GME)-like, extended (e)
SDRs. This subgroup of NDP-sugar
epimerase/dehydratases are extended SDRs; they have the
characteristic active site tetrad, and an NAD-binding
motif: TGXXGXX[AG], which is a close match to the
canonical NAD-binding motif. Members include
Arabidopsis thaliana GDP-mannose-3',5'-epimerase (GME)
which catalyzes the epimerization of two positions of
GDP-alpha-D-mannose to form GDP-beta-L-galactose.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 328
Score = 31.7 bits (72), Expect = 0.52
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 49 QTIFITGATGFLGSLLVEKLLR 70
Q +TGA GF+GS L E+L
Sbjct: 1 QRALVTGAGGFIGSHLAERLKA 22
>gnl|CDD|187672 cd09812, 3b-HSD_like_1_SDR_e, 3beta-hydroxysteroid dehydrogenase
(3b-HSD)-like, subgroup1, extended (e) SDRs. An
uncharacterized subgroup of the 3b-HSD-like extended-SDR
family. Proteins in this subgroup have the
characteristic active site tetrad and NAD(P)-binding
motif of extended-SDRs. 3 beta-HSD catalyzes the
oxidative conversion of delta 5-3 beta-hydroxysteroids
to the delta 4-3-keto configuration; this activity is
essential for the biosynthesis of all classes of
hormonal steroids. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid sythase have
a GGXGXXG NAD(P)-binding motif and an altered active
site motif (YXXXN). Fungal type ketoacyl reductases have
a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 339
Score = 31.7 bits (72), Expect = 0.56
Identities = 45/204 (22%), Positives = 78/204 (38%), Gaps = 48/204 (23%)
Query: 165 RDEELL---ISQTTIIFHIAA---TVRFDEHIRTAYNINVKGTQTILALAKRMKGLKSFV 218
RD L ++ +FHIA+ + R + INV+GT+ I+ + R + + +
Sbjct: 50 RDLSQLEKAVAGVDCVFHIASYGMSGREQLNRELIEEINVRGTENIIQVCVRRR-VPRLI 108
Query: 219 HVSTAYCNCDRKFIAEKFYPPVFTAEELSALVAHASDEEIALLNEHIIGGKPNSYTLTKA 278
+ ST + +F + + DE + L + + Y+ TK+
Sbjct: 109 YTST--------------FNVIFGGQPI-----RNGDESLPYLPLDL---HVDHYSRTKS 146
Query: 279 TAEDLVRQV-GHELP-------ICVLRPSIVF-PTLQEPMPLWIKGFNGVMALALGAGTG 329
AE LV + LP C LRP+ ++ P Q +P + G
Sbjct: 147 IAEQLVLKANNMPLPNNGGVLRTCALRPAGIYGPGEQRHLPRIVSYIE----------KG 196
Query: 330 LIRVVQTDPNISMDVVPGDRVINA 353
L V DP ++ V D ++ A
Sbjct: 197 LFMFVYGDPKSLVEFVHVDNLVQA 220
>gnl|CDD|200085 TIGR01214, rmlD, dTDP-4-dehydrorhamnose reductase. This enzyme
catalyzes the last of 4 steps in making dTDP-rhamnose, a
precursor of LPS core antigen, O-antigen, etc [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 287
Score = 31.2 bits (71), Expect = 0.68
Identities = 13/52 (25%), Positives = 19/52 (36%), Gaps = 5/52 (9%)
Query: 176 IIFHIAATVRFDE---HIRTAYNINVKGTQTILALAKRMKGLKSFVHVSTAY 224
+ + AA D A+ +N Q + A R VH+ST Y
Sbjct: 53 AVVNTAAYTDVDGAESDPEKAFAVNALAPQNLARAAARHGA--RLVHISTDY 102
>gnl|CDD|187566 cd05256, UDP_AE_SDR_e, UDP-N-acetylglucosamine 4-epimerase,
extended (e) SDRs. This subgroup contains
UDP-N-acetylglucosamine 4-epimerase of Pseudomonas
aeruginosa, WbpP, an extended SDR, that catalyzes the
NAD+ dependent conversion of UDP-GlcNAc and UDPGalNA to
UDP-Glc and UDP-Gal. This subgroup has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 304
Score = 31.0 bits (71), Expect = 0.78
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 51 IFITGATGFLGSLLVEKLLR 70
+ +TG GF+GS LVE+LL
Sbjct: 2 VLVTGGAGFIGSHLVERLLE 21
>gnl|CDD|187671 cd09811, 3b-HSD_HSDB1_like_SDR_e, human 3beta-HSD (hydroxysteroid
dehydrogenase) and HSD3B1(delta 5-delta
4-isomerase)-like, extended (e) SDRs. This extended-SDR
subgroup includes human 3 beta-HSD/HSD3B1 and C(27)
3beta-HSD/ [3beta-hydroxy-delta(5)-C(27)-steroid
oxidoreductase; HSD3B7], and related proteins. These
proteins have the characteristic active site tetrad and
NAD(P)-binding motif of extended SDRs. 3 beta-HSD
catalyzes the oxidative conversion of delta 5-3
beta-hydroxysteroids to the delta 4-3-keto
configuration; this activity is essential for the
biosynthesis of all classes of hormonal steroids. C(27)
3beta-HSD is a membrane-bound enzyme of the endoplasmic
reticulum, it catalyzes the isomerization and oxidation
of 7alpha-hydroxylated sterol intermediates, an early
step in bile acid biosynthesis. Mutations in the human
gene encoding C(27) 3beta-HSD underlie a rare autosomal
recessive form of neonatal cholestasis. Extended SDRs
are distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid sythase have
a GGXGXXG NAD(P)-binding motif and an altered active
site motif (YXXXN). Fungal type ketoacyl reductases have
a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 354
Score = 31.3 bits (71), Expect = 0.82
Identities = 29/139 (20%), Positives = 47/139 (33%), Gaps = 37/139 (26%)
Query: 176 IIFHIAATVRFD--EHIRTAYNINVKGTQTILALAKRMKGLKSFVHVST---AYCNCDRK 230
++ H AA V + +NV GTQ +L + +K V+ S+ A N +
Sbjct: 75 VVIHTAAIVDVFGPPNYEELEEVNVNGTQAVLEACVQ-NNVKRLVYTSSIEVAGPNFKGR 133
Query: 231 FIAEKFYPPVFTAEELSALVAHASDEEIALLNEHIIGGKPNSYTLTKATAEDLVRQV--- 287
P+F E+ + Y +K AE++V
Sbjct: 134 --------PIFNG-----------VEDTPYEDTS-----TPPYASSKLLAENIVLNANGA 169
Query: 288 ----GHELPICVLRPSIVF 302
G L C LRP ++
Sbjct: 170 PLKQGGYLVTCALRPMYIY 188
Score = 27.9 bits (62), Expect = 9.1
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 53 ITGATGFLGSLLVEKLLRCCPQIRKIILL 81
+TG GFLG ++ LL ++++I +L
Sbjct: 4 VTGGGGFLGQHIIRLLLERKEELKEIRVL 32
>gnl|CDD|187550 cd05239, GDP_FS_SDR_e, GDP-fucose synthetase, extended (e) SDRs.
GDP-fucose synthetase (aka 3, 5-epimerase-4-reductase)
acts in the NADP-dependent synthesis of GDP-fucose from
GDP-mannose. Two activities have been proposed for the
same active site: epimerization and reduction. Proteins
in this subgroup are extended SDRs, which have a
characteristic active site tetrad and an NADP-binding
motif, [AT]GXXGXXG, that is a close match to the
archetypical form. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 300
Score = 31.0 bits (71), Expect = 0.86
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 50 TIFITGATGFLGSLLVEKLLR 70
I +TG G +GS +V L R
Sbjct: 1 KILVTGHRGLVGSAIVRVLAR 21
>gnl|CDD|236500 PRK09405, aceE, pyruvate dehydrogenase subunit E1; Reviewed.
Length = 891
Score = 31.3 bits (72), Expect = 0.95
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 9/38 (23%)
Query: 228 DRKFIAEKF---YPPVFTAEELSALVAHASDEEIALLN 262
D ++ E F YP E ALVA SD++I LN
Sbjct: 332 DGAYVREHFFGKYP------ETKALVADMSDDDIWALN 363
>gnl|CDD|187574 cd05264, UDP_G4E_5_SDR_e, UDP-glucose 4-epimerase (G4E), subgroup
5, extended (e) SDRs. This subgroup partially conserves
the characteristic active site tetrad and NAD-binding
motif of the extended SDRs, and has been identified as
possible UDP-glucose 4-epimerase (aka UDP-galactose
4-epimerase), a homodimeric member of the extended SDR
family. UDP-glucose 4-epimerase catalyzes the
NAD-dependent conversion of UDP-galactose to
UDP-glucose, the final step in Leloir galactose
synthesis. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 300
Score = 30.7 bits (70), Expect = 0.95
Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 8/60 (13%)
Query: 269 KPNS-YTLTKATAEDLVR--QVGHELPICVLRPSIVFPTLQEPMPLWIKGFNGVMALALG 325
P S Y ++K E +R Q + L VLR S + Q P G GV+ +AL
Sbjct: 133 LPISSYGISKLAIEKYLRLYQYLYGLDYTVLRISNPYGPGQRP-----DGKQGVIPIALN 187
>gnl|CDD|233570 TIGR01777, yfcH, TIGR01777 family protein. This model represents
a clade of proteins of unknown function including the
E. coli yfcH protein [Hypothetical proteins,
Conserved].
Length = 291
Score = 30.7 bits (70), Expect = 0.96
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 51 IFITGATGFLGSLLVEKLLR 70
I ITG TGF+G L ++L +
Sbjct: 1 ILITGGTGFIGRALTQRLTK 20
>gnl|CDD|187556 cd05245, SDR_a2, atypical (a) SDRs, subgroup 2. This subgroup
contains atypical SDRs, one member is identified as
Escherichia coli protein ybjT, function unknown.
Atypical SDRs are distinct from classical SDRs. Members
of this subgroup have a glycine-rich NAD(P)-binding
motif consensus that generally matches the extended
SDRs, TGXXGXXG, but lacks the characteristic active
site residues of the SDRs. This subgroup has basic
residues (HXXXR) in place of the active site motif
YXXXK, these may have a catalytic role. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif
is often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 293
Score = 30.8 bits (70), Expect = 1.0
Identities = 12/26 (46%), Positives = 19/26 (73%)
Query: 51 IFITGATGFLGSLLVEKLLRCCPQIR 76
+ +TGATG++G LV +LL+ Q+R
Sbjct: 1 VLVTGATGYVGGRLVPRLLQEGHQVR 26
>gnl|CDD|218026 pfam04321, RmlD_sub_bind, RmlD substrate binding domain.
L-rhamnose is a saccharide required for the virulence of
some bacteria. Its precursor, dTDP-L-rhamnose, is
synthesised by four different enzymes the final one of
which is RmlD. The RmlD substrate binding domain is
responsible for binding a sugar nucleotide.
Length = 284
Score = 30.7 bits (70), Expect = 1.0
Identities = 11/52 (21%), Positives = 18/52 (34%), Gaps = 5/52 (9%)
Query: 176 IIFHIAATVRFD---EHIRTAYNINVKGTQTILALAKRMKGLKSFVHVSTAY 224
++ + AA D AY +N G + +H+ST Y
Sbjct: 52 VVVNAAAYTAVDKAESEPELAYAVNALGPGNLAEACAARGAP--LIHISTDY 101
>gnl|CDD|187635 cd08930, SDR_c8, classical (c) SDR, subgroup 8. This subgroup
has a fairly well conserved active site tetrad and
domain size of the classical SDRs, but has an atypical
NAD-binding motif ([ST]G[GA]XGXXG). SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 250
Score = 30.4 bits (69), Expect = 1.1
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 47 KDQTIFITGATGFLGSLLVEKLL 69
+D+ I ITGA G +G + LL
Sbjct: 1 EDKIILITGAAGLIGKAFCKALL 23
>gnl|CDD|224015 COG1090, COG1090, Predicted nucleoside-diphosphate sugar
epimerase [General function prediction only].
Length = 297
Score = 30.7 bits (70), Expect = 1.1
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 51 IFITGATGFLGSLLVEKLLR 70
I ITG TG +G L +L +
Sbjct: 1 ILITGGTGLIGRALTARLRK 20
>gnl|CDD|187549 cd05238, Gne_like_SDR_e, Escherichia coli Gne (a
nucleoside-diphosphate-sugar 4-epimerase)-like,
extended (e) SDRs. Nucleoside-diphosphate-sugar
4-epimerase has the characteristic active site tetrad
and NAD-binding motif of the extended SDR, and is
related to more specifically defined epimerases such as
UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), which catalyzes the
NAD-dependent conversion of UDP-galactose to
UDP-glucose, the final step in Leloir galactose
synthesis. This subgroup includes Escherichia coli
055:H7 Gne, a UDP-GlcNAc 4-epimerase, essential for O55
antigen synthesis. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 305
Score = 30.4 bits (69), Expect = 1.4
Identities = 15/32 (46%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 50 TIFITGATGFLGSLLVEKLLRCCPQIRKIILL 81
+ ITGA+GF+G L E+LL P R +IL+
Sbjct: 2 KVLITGASGFVGQRLAERLLSDVPNER-LILI 32
>gnl|CDD|187563 cd05253, UDP_GE_SDE_e, UDP glucuronic acid epimerase, extended
(e) SDRs. This subgroup contains UDP-D-glucuronic acid
4-epimerase, an extended SDR, which catalyzes the
conversion of UDP-alpha-D-glucuronic acid to
UDP-alpha-D-galacturonic acid. This group has the SDR's
canonical catalytic tetrad and the TGxxGxxG NAD-binding
motif of the extended SDRs. Extended SDRs are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 332
Score = 30.4 bits (69), Expect = 1.5
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 50 TIFITGATGFLGSLLVEKLLR 70
I +TGA GF+G + ++LL
Sbjct: 2 KILVTGAAGFIGFHVAKRLLE 22
>gnl|CDD|187578 cd05269, TMR_SDR_a, triphenylmethane reductase (TMR)-like
proteins, NMRa-like, atypical (a) SDRs. TMR is an
atypical NADP-binding protein of the SDR family. It
lacks the active site residues of the SDRs but has a
glycine rich NAD(P)-binding motif that matches the
extended SDRs. Proteins in this subgroup however, are
more similar in length to the classical SDRs. TMR was
identified as a reducer of triphenylmethane dyes,
important environmental pollutants. This subgroup also
includes Escherichia coli NADPH-dependent quinine
oxidoreductase (QOR2), which catalyzes two-electron
reduction of quinone; but is unlikely to play a major
role in protecting against quinone cytotoxicity.
Atypical SDRs are distinct from classical SDRs.
Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 272
Score = 29.9 bits (68), Expect = 1.7
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 51 IFITGATGFLGSLLVEKLLR 70
I +TGATG LG+ +VE LL
Sbjct: 1 ILVTGATGKLGTAVVELLLA 20
>gnl|CDD|233421 TIGR01453, grpIintron_endo, group I intron endonuclease. This
model represents one subfamily of endonucleases
containing the endo/excinuclease amino terminal domain,
pfam01541 at its amino end. A distinct subfamily
includes excinuclease abc subunit c (uvrC). Members of
pfam01541 are often termed GIY-YIG endonucleases after
conserved motifs near the amino end. This subfamily in
This model is found in open reading frames of group I
introns in both phage and mitochondria. The closely
related endonucleases of phage T4: segA, segB, segC,
segD and segE, score below the trusted cutoff for the
family.
Length = 214
Score = 29.7 bits (67), Expect = 2.1
Identities = 23/111 (20%), Positives = 40/111 (36%), Gaps = 13/111 (11%)
Query: 184 VRFDEHIRTAYNINVKGTQTILALAKRMKGLKSFV-HVSTAYCNCDRKFIAEKFYPPVFT 242
R EH++ KG + L A G +F + YCN D E +Y +
Sbjct: 25 KRLKEHLKLLK----KGNRIKLQKALNKYGWSNFSFEILEYYCNKDDLIERETYYIKLLN 80
Query: 243 AEELSALVAHA--------SDEEIALLNEHIIGGKPNSYTLTKATAEDLVR 285
+ ++ A S+E A +++ G K N + + E +
Sbjct: 81 PDAGYNILKIAGSSLGYKHSEETKAKMSKLFSGKKNNPWYGKTHSEETKAK 131
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 29.2 bits (66), Expect = 2.2
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 51 IFITGATGFLGSLLVEKLLR 70
I + GATG G LV++LL
Sbjct: 1 IAVIGATGKTGRRLVKELLA 20
>gnl|CDD|178484 PLN02896, PLN02896, cinnamyl-alcohol dehydrogenase.
Length = 353
Score = 29.8 bits (67), Expect = 2.5
Identities = 12/21 (57%), Positives = 17/21 (80%)
Query: 50 TIFITGATGFLGSLLVEKLLR 70
T +TGATG++GS LV+ LL+
Sbjct: 12 TYCVTGATGYIGSWLVKLLLQ 32
>gnl|CDD|236372 PRK09072, PRK09072, short chain dehydrogenase; Provisional.
Length = 263
Score = 29.5 bits (67), Expect = 2.6
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 47 KDQTIFITGATGFLGSLLVEKLLRC 71
KD+ + +TGA+G +G L E L
Sbjct: 4 KDKRVLLTGASGGIGQALAEALAAA 28
>gnl|CDD|187660 cd08957, WbmH_like_SDR_e, Bordetella bronchiseptica enzymes WbmH
and WbmG-like, extended (e) SDRs. Bordetella
bronchiseptica enzymes WbmH and WbmG, and related
proteins. This subgroup exhibits the active site tetrad
and NAD-binding motif of the extended SDR family. It
has been proposed that the active site in Bordetella
WbmG and WbmH cannot function as an epimerase, and that
it plays a role in O-antigen synthesis pathway from
UDP-2,3-diacetamido-2,3-dideoxy-l-galacturonic acid.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 307
Score = 29.4 bits (66), Expect = 2.8
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 51 IFITGATGFLGSLLVEKLL 69
+ ITG G +GS L+E LL
Sbjct: 3 VLITGGAGQIGSHLIEHLL 21
>gnl|CDD|237079 PRK12367, PRK12367, short chain dehydrogenase; Provisional.
Length = 245
Score = 28.8 bits (65), Expect = 3.4
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 43 QEFYKDQTIFITGATGFLGSLLVEKL 68
Q ++ + I ITGA+G LG L +
Sbjct: 9 QSTWQGKRIGITGASGALGKALTKAF 34
>gnl|CDD|187559 cd05248, ADP_GME_SDR_e, ADP-L-glycero-D-mannoheptose 6-epimerase
(GME), extended (e) SDRs. This subgroup contains
ADP-L-glycero-D-mannoheptose 6-epimerase, an extended
SDR, which catalyzes the NAD-dependent interconversion
of ADP-D-glycero-D-mannoheptose and
ADP-L-glycero-D-mannoheptose. This subgroup has the
canonical active site tetrad and NAD(P)-binding motif.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 317
Score = 29.2 bits (66), Expect = 3.5
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 50 TIFITGATGFLGSLLVEKL 68
I +TG GF+GS LV+ L
Sbjct: 1 MIIVTGGAGFIGSNLVKAL 19
>gnl|CDD|187568 cd05258, CDP_TE_SDR_e, CDP-tyvelose 2-epimerase, extended (e)
SDRs. CDP-tyvelose 2-epimerase is a tetrameric SDR
that catalyzes the conversion of CDP-D-paratose to
CDP-D-tyvelose, the last step in tyvelose biosynthesis.
This subgroup is a member of the extended SDR
subfamily, with a characteristic active site tetrad and
NAD-binding motif. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 337
Score = 29.2 bits (66), Expect = 3.6
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 49 QTIFITGATGFLGSLLVEKLLR 70
+ ITG GF+GS L L+
Sbjct: 1 MRVLITGGAGFIGSNLARFFLK 22
>gnl|CDD|177856 PLN02206, PLN02206, UDP-glucuronate decarboxylase.
Length = 442
Score = 29.2 bits (65), Expect = 3.7
Identities = 36/164 (21%), Positives = 61/164 (37%), Gaps = 64/164 (39%)
Query: 51 IFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYNYFNDAVFDRMRLEC 110
+ +TG GF+GS LV++L+ RG + I V N+F
Sbjct: 122 VVVTGGAGFVGSHLVDRLMA--------------RGDSVIV--VDNFFT----------- 154
Query: 111 PNYADKVDIGITHRVYNYFNDAVFDRMRLECPNYADKVDIVCGQLEADTFGLSARDEELL 170
G V ++F++ F+ +R D+V E +
Sbjct: 155 ---------GRKENVMHHFSNPNFELIRH---------DVV----------------EPI 180
Query: 171 ISQTTIIFHI---AATVRFDEHIRTAYNINVKGTQTILALAKRM 211
+ + I+H+ A+ V + + NV GT +L LAKR+
Sbjct: 181 LLEVDQIYHLACPASPVHYKFNPVKTIKTNVVGTLNMLGLAKRV 224
>gnl|CDD|178263 PLN02657, PLN02657, 3,8-divinyl protochlorophyllide a 8-vinyl
reductase.
Length = 390
Score = 29.0 bits (65), Expect = 3.8
Identities = 11/24 (45%), Positives = 18/24 (75%)
Query: 47 KDQTIFITGATGFLGSLLVEKLLR 70
KD T+ + GATG++G +V +L+R
Sbjct: 59 KDVTVLVVGATGYIGKFVVRELVR 82
>gnl|CDD|233427 TIGR01472, gmd, GDP-mannose 4,6-dehydratase. Alternate name:
GDP-D-mannose dehydratase. This enzyme converts
GDP-mannose to GDP-4-dehydro-6-deoxy-D-mannose, the
first of three steps for the conversion of GDP-mannose
to GDP-fucose in animals, plants, and bacteria. In
bacteria, GDP-L-fucose acts as a precursor of surface
antigens such as the extracellular polysaccharide
colanic acid of E. coli. Excluded from this model are
members of the clade that score poorly because of highly
dervied (phylogenetically long-branch) sequences, e.g.
Aneurinibacillus thermoaerophilus Gmd, described as a
bifunctional GDP-mannose
4,6-dehydratase/GDP-6-deoxy-D-lyxo-4-hexulose reductase
(PUBMED:11096116) [Cell envelope, Biosynthesis and
degradation of surface polysaccharides and
lipopolysaccharides].
Length = 343
Score = 29.0 bits (65), Expect = 4.2
Identities = 25/86 (29%), Positives = 34/86 (39%), Gaps = 15/86 (17%)
Query: 52 FITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSI-TQRVYNYFNDAVFDRMRLEC 110
ITG TG GS L E LL ++ +I R S+S TQR+ + + D
Sbjct: 4 LITGITGQDGSYLAEFLLEKGYEVHGLI-----RRSSSFNTQRIEHIYEDPHNVNKARMK 58
Query: 111 PNYADKVD-------IGIT--HRVYN 127
+Y D D I +YN
Sbjct: 59 LHYGDLTDSSNLRRIIDEIKPTEIYN 84
>gnl|CDD|187575 cd05265, SDR_a1, atypical (a) SDRs, subgroup 1. Atypical SDRs in
this subgroup are poorly defined and have been
identified putatively as isoflavones reductase, sugar
dehydratase, mRNA binding protein etc. Atypical SDRs are
distinct from classical SDRs. Members of this subgroup
retain the canonical active site triad (though not the
upstream Asn found in most SDRs) but have an unusual
putative glycine-rich NAD(P)-binding motif, GGXXXXG, in
the usual location. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 250
Score = 28.8 bits (65), Expect = 4.2
Identities = 9/40 (22%), Positives = 17/40 (42%), Gaps = 1/40 (2%)
Query: 262 NEHIIGGKPNSYTLTKATAEDLVRQVGHELPICVLRPSIV 301
+ + P Y K AED++ + P ++RP +
Sbjct: 118 PDAVGLSDPWDYGRGKRAAEDVLIEA-AAFPYTIVRPPYI 156
>gnl|CDD|176234 cd08273, MDR8, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 331
Score = 28.8 bits (65), Expect = 4.2
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 47 KDQTIFITGATGFLGSLLVE 66
Q + I GA+G +G L+E
Sbjct: 139 TGQRVLIHGASGGVGQALLE 158
>gnl|CDD|181335 PRK08264, PRK08264, short chain dehydrogenase; Validated.
Length = 238
Score = 28.7 bits (65), Expect = 4.4
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 47 KDQTIFITGATGFLGSLLVEKLL 69
K + + +TGA +G VE+LL
Sbjct: 5 KGKVVLVTGANRGIGRAFVEQLL 27
>gnl|CDD|178259 PLN02653, PLN02653, GDP-mannose 4,6-dehydratase.
Length = 340
Score = 29.0 bits (65), Expect = 4.4
Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 5/67 (7%)
Query: 52 FITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYNYFNDAVFDRMRLECP 111
ITG TG GS L E LL ++ II R S TQR+ + + D ++ R++
Sbjct: 10 LITGITGQDGSYLTEFLLSKGYEVHGII----RRSSNFNTQRLDHIYIDPHPNKARMKL- 64
Query: 112 NYADKVD 118
+Y D D
Sbjct: 65 HYGDLSD 71
>gnl|CDD|187580 cd05272, TDH_SDR_e, L-threonine dehydrogenase, extended (e) SDRs.
This subgroup contains members identified as L-threonine
dehydrogenase (TDH). TDH catalyzes the zinc-dependent
formation of 2-amino-3-ketobutyrate from L-threonine via
NAD(H)-dependent oxidation. This group is distinct from
TDHs that are members of the medium chain
dehydrogenase/reductase family. This group has the
NAD-binding motif and active site tetrad of the extended
SDRs. Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 308
Score = 28.8 bits (65), Expect = 4.6
Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 3/46 (6%)
Query: 175 TIIFHIAA--TVRFDEHIRTAYNINVKGTQTILALAKRMKGLKSFV 218
T I H+AA + +++ A+++N+ G +L LA+ L+ FV
Sbjct: 67 TWIIHLAALLSAVGEKNPPLAWDVNMNGLHNVLELAREHN-LRIFV 111
>gnl|CDD|225329 COG2609, AceE, Pyruvate dehydrogenase complex, dehydrogenase (E1)
component [Energy production and conversion].
Length = 887
Score = 29.3 bits (66), Expect = 4.7
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 245 ELSALVAHASDEEIALLN 262
E +ALVA +D++I LN
Sbjct: 343 ETAALVADMTDDDIWALN 360
>gnl|CDD|187652 cd08948, 5beta-POR_like_SDR_a, progesterone 5-beta-reductase-like
proteins (5beta-POR), atypical (a) SDRs. 5beta-POR
catalyzes the reduction of progesterone to
5beta-pregnane-3,20-dione in Digitalis plants. This
subgroup of atypical-extended SDRs, shares the
structure of an extended SDR, but has a different
glycine-rich nucleotide binding motif (GXXGXXG) and
lacks the YXXXK active site motif of classical and
extended SDRs. Tyr-179 and Lys 147 are present in the
active site, but not in the usual SDR configuration.
Given these differences, it has been proposed that this
subfamily represents a new SDR class. Other atypical
SDRs include biliverdin IX beta reductase (BVR-B,aka
flavin reductase), NMRa (a negative transcriptional
regulator of various fungi), phenylcoumaran benzylic
ether and pinoresinol-lariciresinol reductases,
phenylpropene synthases, eugenol synthase,
triphenylmethane reductase, isoflavone reductases, and
others. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. In
addition to the Rossmann fold core region typical of
all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids,
and typically have a TGXXGXXG cofactor binding motif.
Complex (multidomain) SDRs such as ketoreductase
domains of fatty acid synthase have a GGXGXXG
NAD(P)-binding motif and an altered active site motif
(YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 308
Score = 28.8 bits (65), Expect = 4.8
Identities = 15/46 (32%), Positives = 19/46 (41%)
Query: 52 FITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGSTSITQRVYNY 97
+ GATG G LVE LL K+ L R T R+ +
Sbjct: 3 LVVGATGISGWALVEHLLSDPGTWWKVYGLSRRPLPTEDDPRLVEH 48
>gnl|CDD|224012 COG1087, GalE, UDP-glucose 4-epimerase [Cell envelope biogenesis,
outer membrane].
Length = 329
Score = 28.7 bits (65), Expect = 5.6
Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 11/82 (13%)
Query: 165 RDEELL---ISQTTI--IFHIAATVRFDEHIR---TAYNINVKGTQTILALAKRMKGLKS 216
D LL + I + H AA++ E ++ Y+ NV GT ++ + G+K
Sbjct: 54 LDRALLTAVFEENKIDAVVHFAASISVGESVQNPLKYYDNNVVGTLNLIEAMLQT-GVKK 112
Query: 217 FVHVSTA--YCNCDRKFIAEKF 236
F+ STA Y I+E
Sbjct: 113 FIFSSTAAVYGEPTTSPISETS 134
>gnl|CDD|238975 cd02017, TPP_E1_EcPDC_like, Thiamine pyrophosphate (TPP) family, E1
of E. coli PDC-like subfamily, TPP-binding module;
composed of proteins similar to the E1 component of the
Escherichia coli pyruvate dehydrogenase multienzyme
complex (PDC). PDC catalyzes the oxidative
decarboxylation of pyruvate and the subsequent
acetylation of coenzyme A to acetyl-CoA. The E1
component of PDC catalyzes the first step of the
multistep process, using TPP and a divalent cation as
cofactors. E. coli PDC is a homodimeric enzyme.
Length = 386
Score = 28.4 bits (64), Expect = 5.9
Identities = 15/43 (34%), Positives = 19/43 (44%), Gaps = 9/43 (20%)
Query: 223 AYCNCDRKFIAEKF---YPPVFTAEELSALVAHASDEEIALLN 262
D ++ E F YP EL ALV SDE++ LN
Sbjct: 250 TLKAKDGAYVREHFFGKYP------ELKALVTDLSDEDLWALN 286
>gnl|CDD|187659 cd08956, KR_3_FAS_SDR_x, beta-ketoacyl reductase (KR) domain of
fatty acid synthase (FAS), subgroup 3, complex (x).
Ketoreductase, a module of the multidomain polyketide
synthase (PKS), has 2 subdomains, each corresponding to
a SDR family monomer. The C-terminal subdomain catalyzes
the NADPH-dependent reduction of the beta-carbonyl of a
polyketide to a hydroxyl group, a step in the
biosynthesis of polyketides, such as erythromycin. The
N-terminal subdomain, an interdomain linker, is a
truncated Rossmann fold which acts to stabilizes the
catalytic subdomain. Unlike typical SDRs, the isolated
domain does not oligomerize but is composed of 2
subdomains, each resembling an SDR monomer. The active
site resembles that of typical SDRs, except that the
usual positions of the catalytic Asn and Tyr are
swapped, so that the canonical YXXXK motif changes to
YXXXN. Modular PKSs are multifunctional structures in
which the makeup recapitulates that found in (and may
have evolved from) FAS. In some instances, such as
porcine FAS, an enoyl reductase (ER) module is inserted
between the sub-domains. Fatty acid synthesis occurs via
the stepwise elongation of a chain (which is attached to
acyl carrier protein, ACP) with 2-carbon units.
Eukaryotic systems consists of large, multifunctional
synthases (type I) while bacterial, type II systems, use
single function proteins. Fungal fatty acid synthesis
uses a dodecamer of 6 alpha and 6 beta subunits. In
mammalian type FAS cycles, ketoacyl synthase forms
acetoacetyl-ACP which is reduced by the NADP-dependent
beta-KR, forming beta-hydroxyacyl-ACP, which is in turn
dehydrated by dehydratase to a beta-enoyl intermediate,
which is reduced by NADP-dependent beta- ER. Polyketide
synthesis also proceeds via the addition of 2-carbon
units as in fatty acid synthesis. The complex SDR
NADP-binding motif, GGXGXXG, is often present, but is
not strictly conserved in each instance of the module.
This subfamily includes KR domains found in many
multidomain PKSs, including six of seven Sorangium
cellulosum PKSs (encoded by spiDEFGHIJ) which
participate in the synthesis of the polyketide scaffold
of the cytotoxic spiroketal polyketide spirangien. These
seven PKSs have either a single PKS module (SpiF), two
PKR modules (SpiD,-E,-I,-J), or three PKS modules
(SpiG,-H). This subfamily includes the second KR domains
of SpiE,-G, I, and -J, both KR domains of SpiD, and the
third KR domain of SpiH. The single KR domain of SpiF,
the first and second KR domains of SpiH, the first KR
domains of SpiE,-G,- I, and -J, and the third KR domain
of SpiG, belong to a different KR_FAS_SDR subfamily.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
prostaglandin dehydrogenase (PGDH) numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107,
PGDH numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type KRs have
a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 448
Score = 28.4 bits (64), Expect = 6.5
Identities = 16/37 (43%), Positives = 23/37 (62%), Gaps = 2/37 (5%)
Query: 50 TIFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRG 86
T+ ITG TG LG+LL L+ +R ++L+ R RG
Sbjct: 195 TVLITGGTGTLGALLARHLVT-EHGVRHLLLVSR-RG 229
>gnl|CDD|236216 PRK08277, PRK08277, D-mannonate oxidoreductase; Provisional.
Length = 278
Score = 28.3 bits (64), Expect = 6.6
Identities = 10/31 (32%), Positives = 14/31 (45%)
Query: 41 PIQEFYKDQTIFITGATGFLGSLLVEKLLRC 71
P K + ITG G LG + ++L R
Sbjct: 3 PNLFSLKGKVAVITGGGGVLGGAMAKELARA 33
>gnl|CDD|233117 TIGR00759, aceE, pyruvate dehydrogenase E1 component, homodimeric
type. Most members of this family are pyruvate
dehydrogenase complex, E1 component. Note: this family
was classified as subfamily rather than equivalog
because it includes a counterexample from Pseudomonas
putida, MdeB, that is active as an E1 component of an
alpha-ketoglutarate dehydrogenase complex rather than a
pyruvate dehydrogase complex. The second pyruvate
dehydrogenase complex E1 protein from Alcaligenes
eutrophus, PdhE, complements an aceE mutant of E. coli
but is not part of a pyruvate dehydrogenase complex
operon, is more similar to the Pseudomonas putida MdeB
than to E. coli AceE, and may have also have a different
primary specificity.
Length = 885
Score = 28.6 bits (64), Expect = 6.7
Identities = 15/38 (39%), Positives = 18/38 (47%), Gaps = 9/38 (23%)
Query: 228 DRKFIAEKF---YPPVFTAEELSALVAHASDEEIALLN 262
D ++ E F P EL ALVA SD +I LN
Sbjct: 326 DGAYVREHFFNRTP------ELKALVADMSDADIWALN 357
>gnl|CDD|237267 PRK13012, PRK13012, 2-oxoacid dehydrogenase subunit E1;
Provisional.
Length = 896
Score = 28.4 bits (64), Expect = 8.3
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 244 EELSALVAHASDEEIALLN 262
EL+ALVAH SDE+I L
Sbjct: 353 PELAALVAHLSDEDIDRLK 371
>gnl|CDD|215720 pfam00106, adh_short, short chain dehydrogenase. This family
contains a wide variety of dehydrogenases.
Length = 167
Score = 27.5 bits (62), Expect = 8.8
Identities = 13/35 (37%), Positives = 17/35 (48%), Gaps = 2/35 (5%)
Query: 50 TIFITGATGFLGSLLVEKLLRCCPQIRKIILLIRT 84
T+ ITG TG LG L L R ++L+ R
Sbjct: 2 TVLITGGTGGLGLALARWLAA--EGARHLVLVSRR 34
>gnl|CDD|187612 cd05354, SDR_c7, classical (c) SDR, subgroup 7. These proteins
are members of the classical SDR family, with a
canonical active site triad (and also an active site
Asn) and a typical Gly-rich NAD-binding motif. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is
not generally found among SDRs.
Length = 235
Score = 27.8 bits (62), Expect = 9.1
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 47 KDQTIFITGATGFLGSLLVEKLLRCCPQIRKIILLIRTRGST 88
KD+T+ +TGA +G VE LL +K+ +R GS
Sbjct: 2 KDKTVLVTGANRGIGKAFVESLLA--HGAKKVYAAVRDPGSA 41
>gnl|CDD|176232 cd08271, MDR5, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 325
Score = 28.0 bits (63), Expect = 9.3
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 47 KDQTIFITGATGFLGSLLV 65
+TI ITG G +GS V
Sbjct: 141 AGRTILITGGAGGVGSFAV 159
>gnl|CDD|178047 PLN02427, PLN02427, UDP-apiose/xylose synthase.
Length = 386
Score = 27.9 bits (62), Expect = 9.6
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 50 TIFITGATGFLGSLLVEKLL 69
TI + GA GF+GS L EKL+
Sbjct: 16 TICMIGAGGFIGSHLCEKLM 35
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.323 0.139 0.415
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,262,097
Number of extensions: 1925328
Number of successful extensions: 1979
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1952
Number of HSP's successfully gapped: 141
Length of query: 366
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 268
Effective length of database: 6,590,910
Effective search space: 1766363880
Effective search space used: 1766363880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 60 (26.9 bits)